Freesurfer November 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
127 discussions

Help with generation of surface after WM edits
by Krishna Srihasam 30 Nov '10

30 Nov '10

Hi, I am trying to generate surfaces of a monkey brain and I have run into some problem after the initial surface creation. I had some problems with wm.mgz and I corrected them (check the two images I have attached). I then ran recon-all -autorecon2-wm -subjid George -noaseg -xopts-use -nocortribbon The pial and wm surfaces output was exactly similar to the older one (i.e. before the white matter edits).I , then, tried running recon-all with recon-all -autorecon2-pial -subjid George -noaseg -xopts-use -nocortribbon with pretty much the same result. Any help , suggestions or input is more that welcome. Regards, Krishna

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recon-all fsaverage error and re-running
by Joakim Vinberg 30 Nov '10

30 Nov '10

Hi everybody, I received the following error running recon-all on a new subject. It looks like the directory this subject was moved to didn't have the fsaverage link, and so it didn't quite complete. I've replaced the link, and am going to finish processing this subject. My question is: based on the error below and reading ReconAllDevTable, I believe I only have to re-run the final few steps, all in autorecon3. Is this correct, or should I re-run earlier steps as well? Thanks in advance for all of your help! Joakim #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Wed Nov 24 20:40:47 EST 2010 mris_preproc --s 9211 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh ERROR: cannot find fsaverage in /data/freesurfer/round5

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Run skullstrip only?
by Lisa F. Akiyama 30 Nov '10

30 Nov '10

Hello FreeSurfers, By reading through the wiki, it seems like the skullstrip command uses nu.mgz and T1.mgz, but is there a way to just run the skullstrip command without nuintensitycor or normalization? I have MRIs of a few subjects in which the intensity normalization seems to not have beneficial for preparing the MRIs for skullstripping. I've attached the snapshot of brainmask.mgz to this email. Thanks in advance. Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington P Please consider the environment before printing this e-mail.

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recon-all exited with ERRORS
by Zhangyuanchao 30 Nov '10

30 Nov '10

Dear expert， We compute the MRI data with FREESURFER using instruction recon-all -s < > -all,but some data will show recon -all exited with ERRORS in the recon-all-status.log. The flowing display error information :status file for recon-allThu Nov 11 19:22:13 HKT 2010recon-all finished without error at Thu Nov 11 19:22:17 HKT 2010 New invocation of recon-all status file for recon-allThu Nov 11 20:26:17 HKT 2010#@# MotionCor Thu Nov 11 20:26:17 HKT 2010#@# Nu Intensity Correction Thu Nov 11 20:26:33 HKT 2010#@# Talairach Thu Nov 11 20:26:57 HKT 2010#@# Talairach Failure Detection Thu Nov 11 20:27:50 HKT 2010#@# Intensity Normalization Thu Nov 11 20:27:50 HKT 2010#@# Skull Stripping Thu Nov 11 20:31:17 HKT 2010Linux ccm.web 2.6.18-194.17.1.el5xen #1 SMP Wed Sep 29 13:30:21 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Nov 11 23:17:40 HKT 2010 OR LIKE THIS: status file for recon-allThu Nov 11 19:33:11 HKT 2010recon-all finished without error at Thu Nov 11 19:33:15 HKT 2010 New invocation of recon-all status file for recon-allMon Nov 22 00:51:21 HKT 2010#@# MotionCor Mon Nov 22 00:51:21 HKT 2010#@# Nu Intensity Correction Mon Nov 22 00:51:37 HKT 2010#@# Talairach Mon Nov 22 00:52:34 HKT 2010#@# Talairach Failure Detection Mon Nov 22 00:53:20 HKT 2010#@# Intensity Normalization Mon Nov 22 00:53:20 HKT 2010#@# Skull Stripping Mon Nov 22 00:56:37 HKT 2010#@# EM Registration Mon Nov 22 02:36:07 HKT 2010#@# CA Normalize Mon Nov 22 03:17:48 HKT 2010#@# CA Reg Mon Nov 22 03:20:05 HKT 2010#@# CA Reg Inv Mon Nov 22 07:03:03 HKT 2010#@# Remove Neck Mon Nov 22 07:04:31 HKT 2010#@# SkullLTA Mon Nov 22 07:06:08 HKT 2010#@# SubCort Seg Mon Nov 22 08:12:28 HKT 2010Linux ccm.web 2.6.18-194.17.1.el5xen #1 SMP Wed Sep 29 13:30:21 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Nov 22 08:35:10 HKT 2010 Could you explain to me the reason for the problem and could you solve me the problem? I will appreciate your help very much. Best regards, Liang Gao

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mc-sess in freesurfer 5.0
by Luis Lafer-Sousa 29 Nov '10

29 Nov '10

We are having an issue with scripts we used in freesurfer 4.5.0 but no longer work in 5.0.0. It is the mc-sess step, and we receive: ERROR: Flag -toff unrecognized. -sf sf -df df -fsd bold -rlf ./tmp_run_list -toff 0 Done... On the wiki, that flag is still recognized. When we delete it, we then receive a "by run" or "by session" error. I suspect this has something to do with the freesurfer or AFNI update, but we do not know what the new mc-sess takes as tags since the wiki has not changed. Does anybody know how mc-sess has changed? Thank you, Luis L.S.

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qdec analysis and covariates
by Roser Sala 29 Nov '10

29 Nov '10

Hi, We are doing a group analysis using qdec with two groups, and we would like to include gender and age as covariates. Which is the best option in order to perform a simple t-test (group1>group2 and group2>group1) and including the two covariates? (we would like them to have 'zero' weighting in the contrast matrix) We realized that if we include 'age' as a continous factor in the dialog, qdec is performing rather an interaction analysis than a covariate. So, would it be ok to include group and gender as fixed factors and age as nuisance, and then select the output as 'Does the average thickness accounting for gender differ between group1 and group2' (age as nuisance variable)? By checking all the possibilities this seemed the best option for us, but we would like to get a confirmation that we are doing it right. Many thanks Roser

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mri_compute_seg_overlap vs. mri_compute_overlap
by Jeff Dewey 27 Nov '10

27 Nov '10

Hi all, I'm using mri_compute_seg_overlap to calculate dice coefficients for two asegs, and the numbers look reasonable. However, for two of my comparisons, mri_compute_overlap reports zero overlapping voxels between the segmentations. Do these two commands compute overlapping voxels in a different way? Is there another reason why these two commands might report conflicting information? Thanks much for any advice, Jeff

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how to overlap two signicant regions together
by keepmoon 26 Nov '10

26 Nov '10

Dear everyone, Anyone knows how to display overlap regions of two significant changes in one image ? For example, I got the significantly different regions of thickness and curv between patients and controls. Normally we can display them seperately, but now I want to display them together so that I can see clearly where thickness and curv have the same changing regions and where just thickness changes or just curv changes. I will be very appreciated if anyone gives me some advice! Thanks! Joe

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Feeding more than one MPRAGE into recon all
by Arman Eshaghi 25 Nov '10

25 Nov '10

Dear freesurfer experts, Sorry to bother the list with this question again, but I searched the archive and documentation without success. I want to feed more than one MPRAGE datasets taken independently in a single session into recon all. How should I do that? Is there any command inside freesurfer for averaging dcm files? Hoping for an answer and gratefully All the best, Arman

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Brain Segmentation Volume Without Ventricles
by Mailinglisten Lifeandbrain 25 Nov '10

25 Nov '10

Dear ladies and gentlemen, unfortunately the new version (5.0.0) does not compute the Brain Segmentation Volume Without Ventricles in the aseg.stats file any more. Is it possible to fix this problem? Kind regards, Dr. med. Jan Wagner University of Bonn Department of Epileptology Sigmund-Freud-Str. 25 53127 Bonn phone +49 (0)228-287-76140 fax +49 (0)228-287-76261 mail jan.wagner(a)ukb.uni-bonn.de

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Freesurfer November 2010