Freesurfer

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30089 discussions

hippo_subfields atlas
by Rajapillai Pillai 31 Jul '13

31 Jul '13

Dear Freesurfers, I'm have a question regarding the GEMS hippocampal segmentation. I saw on the wiki how to run -hippo_subfields, but how do I access the atlas itself? What file is it under. Also, I'm not sure if I'm missing some files: whenever I try to do one of the individual commands using, for example, posterior_Right_Hippocampus.mgz, it gives the following error: volumeInVoxels: terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file: posterior_Right-Hippocampus.mgz Abort trap Also, upon searching through my freesurfer directory, I cannot find any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz files. Thanks very much for your time, Raja

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Using gcut multiple times
by Chris Watson 31 Jul '13

31 Jul '13

Hello, Is there any value in running recon-all with "-gcut" multiple times? e.g. in a case where skull/dura continues to be left on brainmask.mgz? Thanks, Chris

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White matter edits
by lexi bryon 31 Jul '13

31 Jul '13

Dear Freesurfer experts, I am running recon-all on child brains and I am have an issue with one brain. One entire temporal gyrus is being excluded from the white matter boundary line. I have entered control points and rerun recon-all using autorecon2-cp. This added the desired white matter to wm.mgz: see attached photo. But as you can see it does not recognize it as white matter and/or create the correct white matter boundary/ pial surface. Any ideas? Sincerely, Alexarae

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freesurfer 5.3 T2 flags error
by Joana Braga Pereira 31 Jul '13

31 Jul '13

Dear FreeSurfers, I tried using FreeSurfer 5.3 with the new T2 flags and I got the following error: INFO: Reading transformation from file /tmp/1b2003d0-08c9-4e48-9e9d-622f29f0ff44/mri/transforms/T2raw.lta... Reading transform with LTAreadEx() No such file or directory ERROR: Reading transform from file /tmp/1b2003d0-08c9-4e48-9e9d-622f29f0ff44/mri/transforms/T2raw.lta Linux pe01 3.5.0-27-generic #46~precise1-Ubuntu SMP Tue Mar 26 19:33:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux This is the command I used: /usr/local/freesurfer-5.3/bin/recon-all -T2 0517a9f6-098e-47e8-9038-347d8ec7f840/PPMI_3557_MR_Axial_PD-T2_TSE__br_raw_20110406143102862_49_S103376_I226466.dcm -i 1d58a0ab-3be7-4f18-974a-7faed908c840/MR_MPRAGE_GRAPPA__br_raw_20110406143100268_1_S103377_I226467.dcm -subjid 1b2003d0-08c9-4e48-9e9d-622f29f0ff44 -all -mprage -nuintensitycor-3T -qcache -T2pial Does anyone know why I got this error with the T2 or what I did wrong? Many thanks! joana

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GLM Analysis: ROI (--label)
by Rachel Jonas 30 Jul '13

30 Jul '13

Hi FreeSurfer users, I am running a GLM analysis on the command line, and would like to look specifically within an ROI. I added the flag: --label lh.orbitofrontal.label, in my case, to mri_glmfit, but keep getting an error. It seems that whenever it hits this line in the command, it quits. If I put this flag at the very end (after I specify the glmdir, which I do at the very end), it'll just complete the analysis as if this flag wasn't even there, resulting in a full-brain analysis. Am I missing something here re: how to add in this flag? Any help would be much appreciated! Rachel Jonas

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Cerebellar parcellation
by charles laidi 30 Jul '13

30 Jul '13

Dear Freesurfers, I would like to perform cerebellar parcellation on structural mri with freesurfer. I asked if this was possible 6 months ago (see message below, saying that this feature wasn't available for now). I checked on freesurfer wiki the release notes about Freesurfer version 5.2.0 saying that new cortical parcellations and label were available. "Cortical, Cerebellar, Striatum Parcellation in MNI152 space found in average/<Yeo_JNeurophysiol11_MNI152>, average/<Buckner_JNeurophysiol11_MNI152> and average/<Choi_JNeurophysiol12_MNI152>. See README file in each directory for more details. Note that these README files will be updated to reflect minor improvements in parcellations beyond the publication wikipages". My understanding is that cerebellar parcellation on structural mri is still not available, could you tell me if I'm right ? When I'm checking the link on the release notes it doesn't seems to concern structural imaging. Thanks a lot for your attention, sorry if my question seems obvious but I'm not very familiar with freesurfer. Charles PS : -answer : Hi Charles, that is true at the moment, although we are working on something that should be ready relatively soon. cheers Bruce -question : Dear freesurfer, I'm trying to perform parcellation on the cerebellum. After reading closely freesurfer wiki and the questions related to this topic on the mailing list, my understanding is that there is no way to perform fully automted cerebellar parcellation on structural mri with freesurfer. Could you tell me if I'm right ? Thanks a lot for your attention Charles

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are many *.dat files written out to disk in <subj_dir>/mri and then deleted when autorecon completes?
by Montillo, Albert (GE Global Research) 30 Jul '13

30 Jul '13

After importing a subject's data (T1 single time point) I run a script with these commands: recon-all -s <subject> -autorecon1 recon-all -s <subject> -autorecon2 recon-all -s <subject> -autorecon3 I did this twice, once on each of two linux machines. I am using the same exact input intensity T1 data and importing the data into separate subject names (e1859_workingBak and e1858_nonworking) so there is no collision. Why am I getting many (really 1000's ) of v1_1.dat files in the $SUBJECTS_DIR/<subject>/mri of one of the machines, even though the input data is the same? They are named vNNN_N.dat where N is a digit . Contents of one of these files is below. The contents of the subject folders are represented below using the du -k . command. Now in this nonworking case the job terminated early (run time limit on the job which I can fix ) ; however I am curious: are all of these *.dat files (40GB worth!) written out all the time and then deleted at the end of the recon tasks? This happens on one red-hat linux machine (cluster ) but not on another for the same subject data Is this normal behavior? Are the dat files written out normally and then deleted later in the processing (since I don't see them in the run that completed). Contents of a subject after a successful run to completion: [e1858_workingBak]$ du -k . 1176 ./scripts 16 ./mri/transforms/bak 108200 ./mri/transforms 14088 ./mri/orig 176068 ./mri 149940 ./surf 16 ./tmp 35228 ./label 1096 ./touch 544 ./stats 16 ./src 16 ./trash 16 ./bem 364132 . Contents of same MRI input data to a different subject name, whose processing (same as above) terminated prematurely: [e1858_nonworking]$ du -k . 800 ./scripts 16 ./mri/transforms/bak 108200 ./mri/transforms 14088 ./mri/orig 41027804 ./mri 29252 ./surf 16 ./tmp 16 ./label 360 ./touch 16 ./stats 16 ./src 16 ./trash 16 ./bem 41058328 . This is when the processing of e1858_nonworking got terminated: [scripts]$ tail recon-all-status.log #@# Intensity Normalization2 Thu Jul 25 19:20:22 EDT 2013 #@# Mask BFS Thu Jul 25 19:24:53 EDT 2013 #@# WM Segmentation Thu Jul 25 19:24:56 EDT 2013 #@# Fill Thu Jul 25 19:27:47 EDT 2013 #@# Tessellate lh Thu Jul 25 19:28:47 EDT 2013 #@# Smooth1 lh Thu Jul 25 19:28:56 EDT 2013 #@# Inflation1 lh Thu Jul 25 19:29:01 EDT 2013 #@# QSphere lh Thu Jul 25 19:29:37 EDT 2013 #@# Fix Topology lh Thu Jul 25 19:35:03 EDT 2013 #@# Make White Surf lh Thu Jul 25 19:55:20 EDT 2013 This is the contents of one (v1_1.dat ) of the many *.dat files in /mri [mri]$ tail v1_1.dat 12.014513 223.051927 250.208421 12.052258 222.911943 252.203797 12.090005 222.771944 254.199159 12.127751 222.631960 256.194520 12.165498 222.491960 258.189912 12.203243 222.351976 260.185273 12.240990 222.211977 262.180635 12.278736 222.071992 264.175996 12.316483 221.931993 266.171358 12.354229 221.791994 268.166750

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Deformed tksurfer results
by pfotiad＠nmr.mgh.harvard.edu 30 Jul '13

30 Jul '13

Hi, I ran tksurfer (with the inflated surface option) on a couple of my subjects that had a major deformation in their orig.mgz file and the inflated surface of tksurfer looked as if a chunk was missing off of it at the position where the deformation is located. Is that normal? I have attached two images to illustrate what I mean: One of an axial slab of the orig.mgz file where the deformation is shown, and one of the inflated surface of the same subject in tksurfer. Thank you for your time, Panos

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Unsegmented ventricles
by Victor Kovac 30 Jul '13

30 Jul '13

Dear Freesurfer experts, I am running recon-all on very atrophied brains with mixed results. Attached is an image of a brain where segmentation has gone awry. There is no message indicating talairach failure, and the segmentation appears to need WM and pial edits as well as the ventricles to be filled, so I am not sure how to proceed. If you have any recommendations as to how to fix these errors, I would very much appreciate it -- these data are past their deadline, and I am at a loss. Thank you! Sincerely, Victor

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Re: [Freesurfer] Deformed tksurfer results
by pfotiad＠nmr.mgh.harvard.edu 30 Jul '13

30 Jul '13

Sorry forgot the attachments. >> Hi, >> >> I ran tksurfer (with the inflated surface option) on a couple of my >> subjects that had a major deformation in their orig.mgz file and the >> inflated surface of tksurfer looked as if a chunk was missing off of it >> at >> the position where the deformation is located. Is that normal? >> >> I have attached two images to illustrate what I mean: One of an axial >> slab >> of the orig.mgz file where the deformation is shown, and one of the >> inflated surface of the same subject in tksurfer. >> >> Thank you for your time, >> Panos >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >

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