tag:blogger.com,1999:blog-5737874959005852552.post9082560741781435092..comments2023-10-18T16:31:41.080-05:00Comments on MVPA Meanderings: extracting values from CIFTI files: an easier way!Jo Etzelhttp://www.blogger.com/profile/04277620767760987432noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-5737874959005852552.post-11379819368197222002017-07-28T10:34:55.617-05:002017-07-28T10:34:55.617-05:00Hello Jo!
Thank you for your blog.
I am writing...Hello Jo!<br /><br />Thank you for your blog. <br /><br />I am writing you from Spain. I am a Master student and I would like to use some HCP data in my final dissertation. However, I can get these results, I mean:<br /><br />I would like to extract the timeseries of each voxel in the GM and the cartesian coordinate in MNI atlas for each one. Could you help me? I've been some days trying it without success.<br /><br />I tried with these cases:<br />a) wb_command -cifti-convert -to-text /path/tfMRI_MOTOR_LR_Atlas.dtseries.nii /path/timeseries.txt<br /><br />Result: when the process is finished (without error messages) I go to the /path/ and no timeseries.txt is in it.<br /><br />b) wb_command -cifti-convert -to-nifti /path/tfMRI_MOTOR_LR_Atlas.dtseries.nii /path/file.nii.gz<br /><br />But I have as result a nifti file that I don't know how to interpret it:<br />data_type FLOAT32<br />dim1 32767<br />dim2 3<br />dim3 1<br />dim4 284<br />datatype 16<br />pixdim1 1.000000<br />pixdim2 1.000000<br />pixdim3 1.000000<br />pixdim4 1.000000<br /><br /><br />Can I extract these information directly from the tfMRI_MOTOR_LR.nii.gz with FSL (for example) like any other dataset? What is the difference with the wb_commands? For example (to extract all timeseries):<br />fslmeants -i tfMRI_MOTOR_LR.nii.gz -o timeseries.txt -m gm_mask.nii.gz --showall<br /><br />Thank you so much in advance for your help.<br /><br />Best,<br />JP.Anonymoushttps://www.blogger.com/profile/15804821235238408279noreply@blogger.comtag:blogger.com,1999:blog-5737874959005852552.post-53128023955794769522017-06-14T19:17:30.561-05:002017-06-14T19:17:30.561-05:00Right, I forgot about that. It would work on the ...Right, I forgot about that. It would work on the dlabel file. The crashes were from either having only dtseries as input, or if input cifti files had volume structures.<br /><br />These crashes have been fixed in the source repository, but we haven't made a new release in a while. There is a development version available that we update manually, but we don't really advertise it, because scene files saved with a development version may break with a subsequent released version.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-5737874959005852552.post-89997433960786514562017-06-14T16:59:12.128-05:002017-06-14T16:59:12.128-05:00Is -cifti-create-dense-from-template fixed? I trie...Is -cifti-create-dense-from-template fixed? I tried it but ran into core dumps, and saw a few messages that it was broken.Jo Etzelhttps://www.blogger.com/profile/04277620767760987432noreply@blogger.comtag:blogger.com,1999:blog-5737874959005852552.post-4592383700476697122017-06-14T14:58:22.922-05:002017-06-14T14:58:22.922-05:00Instead of relying on surfaces being first in cift...Instead of relying on surfaces being first in cifti files, you can also create a new cifti file containing the parcellation, but which is index-matched to your other files. This is fairly easy to do with wb_command -cifti-create-dense-from-template.<br /><br />You should also consider using the dlabel.nii version instead, especially for viewing in wb_view (because it contains independent colors per-label) and things like "wb_command -cifti-parcellate" that require a label file, rather than just an integer-valued file. While the gordon parcel names are just number-based, the HCP MMP parcels have names based on functional area literature, which makes them easier to keep straight (which is important when there are 180 of them per hemisphere...).Anonymousnoreply@blogger.com