Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

mri_nu_correct error: flar --uchar not recignized
by erbilnurhan 27 Oct '20

27 Oct '20

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to compute volumetric data from MPRAGE images by using recon-all as decribed athttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all I've got the following message: mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 ERROR: flag --uchar not recognized Does anyone have any thoughts on how to trouble-shoot this problem? Also, I've attached the recon-all.log in case it's of any use. FreeSurfer version: freesurfer-darwin-macOS-7.1.1 (freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0) macOS high Sierra 10.13.6, x86_64 XQuartz 2.7.11 (xorg-server 1.18.4) recon-all.log: see attached Sincerely, Nurhan Erbil

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How is Total cortical gray matter volume calculated?
by Ian Hardingham 27 Oct '20

27 Oct '20

External Email - Use Caution Hi Freesurfers, Is "total cortical gray matter volume" from aseg.stats calculated based on the recon-all Surfaces? Or using a different method? I ask because I have been trying to calculate the grey matter volume based on the area between the surfaces, and I have been getting different results. Thanks, Ian

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Issue with extracted thickness value from significant cluster or peak vertex
by Julian Macoveanu 27 Oct '20

27 Oct '20

External Email - Use Caution Hi, I am using FS 7.1.0. After running the surface thickness GLM analysis I get one cluster after correction for multiple comparison showing a significant group difference. I want to make a plot illustrating this group difference. However, when using the mean values from: cache.th30.abs.y.ocn.dat, I don’t see the expected group difference in these values. Question 1) Are the subjects cluster mean values in y.ocn.dat adjusted for the covariates I used in the fsgd file? E.g. age, sex and TIV? Question 2) I inserted these mean cluster values from y.ocn.dat in SPSS and tried verify the statistics both with and without adjustment for covariates and did not get the expected significant group region which I expected in either case. Why is this? Question 3) I moved on to extract the thickness values from peak vertex in my significant cluster. For this I used mris_convert which I just wanted to be confirmed that is correct: mris_convert -c lh.thickness.fwhm15.fsaverage.mgh $freesurferdir/fsaverage/surf/lh.orig output.asc After extracting the thickness value for all subjects from the peak vertex as reported by the sig.cluster.summary , I still have the same issue as before, I find no group expected group difference. Interestingly, the significant cluster I found is part of the superior_frontal region in aparc2009. When I extract these values it almost shows significant group differences in the entire region, in line with the surface GLM findings. Thanks, Julian

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lh.white edits
by Wei Koo 27 Oct '20

27 Oct '20

External Email - Use Caution Hello FreeSurfer Developers, I am trying to make edits to the white matter segmentation. I have tried making edits to wm.mgz and repeating recon2-wm but I was wondering if there is a way to make direct edits to lh.white? I've searched the lists and did not seem to find anything regarding editing the surface directly.

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Display results with tksurfer
by Marina Fernández 27 Oct '20

27 Oct '20

External Email - Use Caution Thanks for the reply Doug, We used the tksurfer command lines because they were run in matlab after performing some analysis to obtain the figures of the results. With the scripts, these figures are automatically saved for later review. We would like to know if what you propose with freeview is appropriate for this and if we can modify the scale of min-max significant t values with the freeview options (I copy the previous message below). Thank you so much for your attention. Best regards, Marina ------------------------------------------------------------------------------------------------------------------------------- Douglas N. Greve <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Mon, 19 Oct 2020 07:50:56 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> Not sure, we don't use tksurfer that much anymore. Have you tried freeview? You can run freeview with tksurferfv and the same tksurfer arguments (makes it easier) On 10/13/2020 5:03 AM, Marina Fernández wrote: External Email - Use Caution Dear Freesurfer experts, I would like to modify the values of the colorbar scale to display results in the inflated surface with tksurfer, in such a way that displayed values in the colorbar range from the minimum t- value detected to the maximum t value detected. I have tried to use the -fminmax flag, but the colorbar scale shows values from 0 to the maximum t value. Is it possible to limit values of the colorbar scale to min-max significant t values? On the other hand, is it possible to invert the colors of the colorbar scale (e.g., red for higher t values and yellow for lower t values)? Thank you in advance. Best regards, Marina _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Issues with transferring edits from v6.0dev into v7.1
by Melanie Ganz 27 Oct '20

27 Oct '20

External Email - Use Caution Dear FS list, as soon as samseg was available in FS v6dev we used it to process some of our data. The plan was always to wait for v7 to use a stable version, but edits were made already on v6FSdev, while we waited last spring for v7 to come out. Now I have been having issues with transferring edits from v6dev into v7.1, which I thought should be a straight forward thing to do. The way I did it, is I ran v7.1 on the raw data, then I copied the files where edits where made, e.g. brainmask.mgz, wm.mgz as well as control.dat. Finally, at this point I reran recon-all -all ( since I actually couldn't get recon-all with the -make flag to work). But I see my rerun fails with the error message: Saving brainmask.auto.mgz Command terminated by signal 11 @#@FSTIME 2020:10:06:14:45:45 mri_watershed N 10 e 20.81 S 1.93 U 22.55 P 117% M 893740 F 0 R 330549 W 0 c 83 w 1353 I 22344 O 2312 L 3.35 3.67 2.94 @#@FSLOADPOST 2020:10:06:14:46:06 mri_watershed N 10 3.10 3.59 2.93 Linux krogh 4.12.14-lp151.28.59-default #1 SMP Wed Aug 5 10:58:34 UTC 2020 (337e42e) x86_64 x86_64 x86_64 GNU/Linux recon-all -s g612_GD exited with ERRORS at Tue Oct 6 14:46:06 CEST 2020 and I don't understand why. The earlier FSrun with v7.1 ran fine and I also tried copying to a separate directory to check file permissions and the same error appears again. I have uploaded the subject to the ftp server at surfer.nmr.mgh.harvard.edu and it's called subject.tar.gz. Kind regards, Melanie -- Yours sincerely Melanie Ganz-Benjaminsen Forsker Direct: + 45 35 45 67 18 Mail: melanie.ganz(a)nru.dk Neurobiology Research Unit Rigshospitalet, building 6931 Juliane Maries Vej 28, 3rd floor DK-2100 Copenhagen, Denmark Phone: +45 3545 6712 Fax: +45 3545 6713 URL:http://nru.dk This e-mail and any attachment may contain confidential and privileged material intended for the addressee only. If you are not the addressee, you are notified that no part of the e-mail or any attachment may be disclosed, copied or distributed, and that any other action related to this e-mail or attachment is strictly prohibited, and may be unlawful. If you have received this e-mail by error, please notify the sender immediately by return e-mail, and delete this message.

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Group Analysis: Comparing four groups
by Steve Petersen 27 Oct '20

27 Oct '20

External Email - Use Caution Dear Freesurfer experts, This is the first time I perform group analysis in Freesurfer. My aim is to compare the cortical thickness in four groups matched in age, sex and years of education using the Monte Carlo multiple comparisons correction. I tried to follow the Freesufer tutorials <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis> to perform this group analysis and I would be really grateful whether someone can verify that all steps are correct. For example, for the cortical thickness (smooth = 15 FWHM) of the left hemisphere, the four steps that I followed were: STEP 1. Assemble the cached Data (mris_preproc) using the fsgd file mris_preproc --fsgd STUDY_4groups.fsgd \ --cache-in thickness.fwhm15.fsaverage \ --target fsaverage \ --hemi lh \ --out lh_J4G_thickness.15.mgh \ STEP 2. Perform a GLM Analysis (mri_glmfit) mri_glmfit \ --y lh_J4G_thickness.15.mgh \ --fsgd STUDY_4groups.fsgd \ --C *group.effect.mtx* \ --surf fsaverage lh \ --cortex \ --glmdir left_hemisphere_thickness_results\ STEP 3. Perform Monte Carlo simulation mri_glmfit-sim \ --glmdir left_hemisphere_thickness_results \ --sim mc-z 10000 4 mc-z.abs \ --sim-sign abs --cwpvalthresh 0.05\ --overwrite \ *QUESTIONS:* 1. Have I followed the steps to perform the analysis correctly or do you think I forgot some important flag? 2. Before test differences between two groups (eg. group1 > group 2 with the vector 1 -1 0 0) I would like to test any group effect. For that purpose, I created the group.effect.mtx contrast file (see below), is correct? 1 -1 0 0 0 1 -1 0 0 0 1 -1 Any help would be appreciated. Best regards, Steve

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LGI output question
by Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience 27 Oct '20

27 Oct '20

External Email - Use Caution Dear Freesurfer experts, I have performed LGI for one of my subject pools and I was wondering if I can compute the mean area for the different LGI values instead of the area in the output tables? How should I edit the code below to accomplish this? Thank you and stay safe! mri_segstats --annot my_subject_id lh aparc --i $SUBJECTS_DIR/my_subject_id/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats All the best, Alex

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surface/volume editing
by Jake Jensen 27 Oct '20

27 Oct '20

External Email - Use Caution Hello, I am attempting to edit a subject, but upon removing voxels where the WM and pial surfaces should not be, the WM surface does not receed (pictures are attached). I have attempted this with -all and -autorecon2, running it again from the original 001.mgz file, as well as attempting to run it from the beginning with -clean. The end result is consistently the same, as seen in the attached images. Additionally, it is strange that the WM surface crosses the pial. I could not seem to find a solution to this in the archives. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: OSX mojave -all -autorecon2 Recon all log attached Thank you! -Jacob

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white and pial surfaces appearing outside gray matter boundary
by Batool Rizvi 27 Oct '20

27 Oct '20

External Email - Use Caution Dear FreeSurfer experts, I'm seeing this type of error reoccur for around half of the subjects I've reviewed so far for a specific study. The pial and white surfaces are merging to the outermost boundary of the brain. Provided that these are older subjects, but I didn't see this error in my experience editing older subjects in other studies. Is there perhaps a preprocessing command I could perform since this error is systematic throughout the brain, not specific to a region? Attached is an example image that showed this type of mislabeling (tried attaching more images but there were size limits). Thank you for any input! [image: 219.png] Batool

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Freesurfer October 2020