Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

Extract the mean cortical thickness of each significant clusters
by Santosh Yadav 16 Jun '14

16 Jun '14

Dear Freesurfer Experts, Please ignore the previous email. I would like the mean thickness measures of each clusters, survived after multiple comparison correction, in qdec. I used qdec for a group comparison in cortical thickness between a patient group and a healthy control group. I found 30 different significant clusters after FDR. I would like to extract the mean cortical thickness of each significant cluster in the patient group and in the healthy control group. I went though previous post and run the following command: mri_glmfit-sim --glmdir lh-Diff-Control-HF-Intercept-thickness --cache 1.3 abs --cwpvalthresh .99 and found following output: cmdline mri_glmfit --y /home/virtualuser/freesurfer/subjects/qdec/glmdir/y.mgh --fsgd /home/virtualuser/freesurfer/subjects/qdec/glmdir/qdec.fsgd doss --glmdir /home/virtualuser/freesurfer/subjects/qdec/glmdir --surf fsaverage lh --label /home/virtualuser/freesurfer/subjects/fsaverage/label/lh.aparc.label --C /home/virtualuser/freesurfer/subjects/qdec/glmdir/contrasts/lh-Avg-Intercept-thickness.mat --C /home/virtualuser/freesurfer/subjects/qdec/glmdir/contrasts/lh-Diff-Control-HF-Intercept-thickness.mat WARNING: unrecognized mri_glmfit cmd option doss SURFACE: fsaverage lh set: No match. FreeSurfer:~/freesurfer/subjects/qdec/glmdir> Please suggest where i can find out the file for thickness. Is above commond is correct? and program showed the warning: unrecognized mri_glmfit cmd option doss. Any help would be great. With regards, Santosh -- With Best Regards, Post Doctoral Fellow, Department of Anesthesiology University of California, Los Angeles, CA 90034 Phone No. 808-5896940

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Extract the mean cortical thickness of each significant clusters
by Santosh Yadav 16 Jun '14

16 Jun '14

Dear Freesurfer Experts, I would like the mean thickness measures of each clusters i found in qdec from both control and patient group. I used qdec for a group comparison in cortical thickness between a patient group and a healthy control group. I found 30 different significant clusters after FDR. I would like to extract the mean cortical thickness of each significant cluster in the patient group and in the healthy control group. I went though previous post and run the following command: mri_glmfit-sim --glmdir lh-Diff-Control-HF-Intercept-thickness --cache 1.3 abs --cwpvalthresh .99 and found following output: cmdline mri_glmfit --y /home/virtualuser/freesurfer/subjects/qdec/glmdir/y.mgh --fsgd /home/virtualuser/freesurfer/subjects/qdec/glmdir/qdec.fsgd doss --glmdir /home/virtualuser/freesurfer/subjects/qdec/glmdir --surf fsaverage lh --label /home/virtualuser/freesurfer/subjects/fsaverage/label/lh.aparc.label --C /home/virtualuser/freesurfer/subjects/qdec/glmdir/contrasts/lh-Avg-Intercept-thickness.mat --C /home/virtualuser/freesurfer/subjects/qdec/glmdir/contrasts/lh-Diff-Control-HF-Intercept-thickness.mat WARNING: unrecognized mri_glmfit cmd option doss SURFACE: fsaverage lh set: No match. FreeSurfer:~/freesurfer/subjects/qdec/glmdir> Any help would be great. With regards, Santosh -- With Best Regards, Post Doctoral Fellow, Department of Anesthesiology University of California, Los Angeles, CA 90034 Phone No. 808-5896940

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Problem of VolumeRoiCorticalThickness
by wangkangcheng_gmail 15 Jun '14

15 Jun '14

Hi all, I want to extract cortical thickness for a ROI (dlpfc) which was defined in volume space. I search it in Freesurfer Wiki and find the description in website (http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) But, in the second, it said it need an T1 volume (average of subjects) which was called TT_avg152T1.nii. How can I calculate it? What is the voxels of ROI and T1.nii, 1*1*1 mm2? Thank you Wang Kangcheng

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Re: [Freesurfer] Substantia Nigra Segmentation
by Katherine Fu 14 Jun '14

14 Jun '14

I was wondering if Freesurfer now segments the substantia nigra, since as of June 2013 it did not? Thank you for your help. Best, Katherine Fu On Sat, Jun 14, 2014 at 10:56 AM, Katherine Fu <kathfu(a)usc.edu> wrote: > I was wondering if Freesurfer now segments the substantia nigra, since as > of June 2013 it did not? > > Thank you for your help. > > Best, > Katherine Fu > > -- > Katherine Fu > Keck School of Medicine of USC > Class of 2017 > kathfu(a)usc.edu > -- Katherine Fu Keck School of Medicine of USC Class of 2017 kathfu(a)usc.edu

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Center vertex of label
by Martijn Steenwijk 14 Jun '14

14 Jun '14

Dear all, I was wondering, is there a way to to find the vertex in the middle of a label? Not in terms of center of gravity of voxels, but on the (spherical?) surface? Looking forward to suggestions, Best, Martijn

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protocol question
by Joshua Lee 13 Jun '14

13 Jun '14

Dear Freesurfer Experts, I am trying to better understand what regions of the hippocampal formation are meant to be included in the hippocampal label (e.g. inclusion of the alveus/fornix, lateral boundaries around the subiculum, superior boundaries in the tail, etc.). Has the protocol used to manually segment the hippocampus for the Freesurfer atlases been described in detail somewhere? I cannot seem to locate a specific reference. Thanks Joshua

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Color scale in TkSurfer
by Zeynep Akalin Acar 13 Jun '14

13 Jun '14

I'm plotting potential distributions on a cortical surface using TkSurfer. The color scale "Heat" gives the most comprehensible plots. However, I would like to have the maximum values to be plotted in red instead of yellow, and minimum in dark blue instead of light blue. max +threshold 0 -threshold min -> Overlay values yellow red gray dark blue light blue -> Heat colorscale red yellow gray light blue dark blue -> Desired colorscale Is there a way to have the color scale like this? I tried the color scales 'green red' and 'blue red', however, when I select these scales the brain surface disappears. Thank you, Zeynep.

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FS GUI no glx extension
by Arman Eshaghi 13 Jun '14

13 Jun '14

Hi, On a remote server forwarding X and running Ubuntu 14.04 I am having difficulty running tkregister2, with this error: * No glx extension!* * register: ### tkoInitWindow(name) failed* Also tried * export LIBGL_ALWAYS_INDIRECT=y* which did not work. Any input is highly appreciated. All the best, Arman

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Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing
by Martin Reuter 13 Jun '14

13 Jun '14

Hi Doug, The second command below should copy your edits from the finalsurf manedit in cross to the long directory. You can try that command manually with a fresh volume. If it really does not carry over, can you send me the two volumes (edited one from cross and the unedited one from long) so that I can take a look. Maybe your edits are wrong (deletes are not zero, but adifferent number, I think 1). Not sure what consequences it has to copy to brainmask but I would not recommend it. Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Douglas Merkitch <Douglas_Merkitch(a)rush.edu> Date:06/05/2014 9:51 PM (GMT+01:00) To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing Hello Martin and FreeSurfer experts, I've checked the recon-all.log from the 2nd tp of one of the longitudinal subject directories (1004_1.long.1004_base) and found the following 4 lines using your search criteria: 1. \n mri_mask -transfer 255 -keep_mask_deletion_edits brainmask.auto.mgz brainmask_1004_base.mgz brainmask.auto.mgz \n 2. \n mri_mask -transfer 255 -keep_mask_deletion_edits -xform /Users/glennstebbins/Desktop/harlow_mount/JenG/ResearchAssistant/data/freesurfer_v5.1/1004_base/mri/transforms/1004_1_to_1004_base.lta brain.finalsurfs.mgz /Users/glennstebbins/Desktop/harlow_mount/JenG/ResearchAssistant/data/freesurfer_v5.1/1004_1/mri/brain.finalsurfs.manedit.mgz brain.finalsurfs.mgz \n 3. \n mri_mask -transfer 255 -keep_mask_deletion_edits -xform /Users/glennstebbins/Desktop/harlow_mount/JenG/ResearchAssistant/data/freesurfer_v5.1/1004_base/mri/transforms/1004_1_to_1004_base.lta wm.mgz /Users/glennstebbins/Desktop/harlow_mount/JenG/ResearchAssistant/data/freesurfer_v5.1/1004_1/mri/wm.mgz wm.mgz \n 4. \n mri_mask -transfer 255 -keep_mask_deletion_edits brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz brain.finalsurfs.mgz \n Does any of this stand out to you? In visually comparing the brain.finalsurfs.manedit.mgz files between the cross and long, the edits do not appear to transfer to the long as has happened previously. However, when the brain.finalsurfs.manedit.mgz file is copied to the brianmask.mgz file (in the base and cross time points), and the longitudinal processes stream is run, the edits now contained in the brainmask.mgz files do seem to transfer. Can you think of any complications (other than cerebellar) that would arise from copying the brain.finalsurfs.manedit.mgz file (where edits were made) to the brainmask.mgz in the cross-sectional and base directories and rerunning the longitudinal processing stream from scratch? Thanks for all your help! Doug Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Douglas_Merkitch(a)rush.edu On May 19, 2014, at 3:52 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: Hi Doug, Usually I edit dura etc in the brainmask and only touch finalsurfs for cerebellum edits. But your way should also work (at least I don't know right now why it should not). Anyway, I looked at recon-all and in the mask BFS step, it does copy the edits over from the cross into the long (if it's working as it should, see line 2565). That command should be printed in your log file of the long run and you can search and double-check that it is there. (mri_mask -transfer 255 -keep_mask_deleting_edits -xform .....) You can also compare the brain_finalsurfs between cross and long in each time point to make sure the edits did get transferred. Be aware that these two images are not registered. The cross is in the original space, the long in the same space as the base and all other time points. So you may have to search around to find the same exact place. Anyway, assuming edits do get through, the finalsurfs is then used in the mris_make_surfaces step. In long, this step is different from cross, as it takes the surfaces from the base as initialization and then fine tunes them. So you also have to check the surfaces in the base are all OK. That is essential as long takes it from there. Best, Martin On 05/16/2014 12:29 PM, Douglas Merkitch wrote: Dear Martin and FreeSurfer experts, Thanks for your response. I have just finished re-running some subjects from scratch in 5.3 and it appears that the edits from brain.finalsurfs.manedit.mgz are not being applied to the longitudinal subject directories. Just to clarify, I have been doing ALL of the pial surface edits in the brain.finalsurfs.manedit.mgz, not just the pial surface edits that have extended into the cerebellum. The rationale for doing this is mainly continuity, as the previous research assistant made all pial surface edits in this way because of a response she had received from the FS forum saying that there shouldn't be any problem with performing all the pial surface edits in the brain.finalsurfs.manedit.mgz file. Is there something in the FreeSurfer longitudinal processing code that would treat edits near the cerebellum of the brain.finalsurfs.manedit.mgz file differently from those made in other parts of the brain (e.g. lateralorbitofrontal, dura, etc.,)? Can you think of anything else that would be causing this or anything that I could try to get the longitudinal processing stream to incorporate the edits from the brain.finalsurfs.manedit.mgz file? Thanks for your help! Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Douglas_Merkitch(a)rush.edu Begin forwarded message: From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing Date: May 2, 2014 4:20:17 PM CDT To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Hi Doug, so you 1. edited the cross sectionals and surfaces look fine (make sure you edit the brain.finalsurfs.manedit.mgz file, which you create as a copy of the brain.finalsurfs.mgz) 2. checked/edited the base and surfaces look fine too 3. ran the longitudinal from scratch (w/o any edits) and then in the long, the surface looks not good? Edits should automatically be copied from cross->long (if the manedit file exist). Surfaces are taken from the base to initialize longitudinal processing. That is why both step1 and step2 above are important. Step3 is a good idea to make sure that the longs are not polluted by some earlier edits. For example edits from cross are only copied over if the long has no manedit file, else only the edits in the long will be used. (I think this also answers some of the questions in the archive mail 1 you cite below, the archive mail 2 is a question about cross sectional processing, but I think there the problem is that brainmask.finalsurfs.mgz was edited directly, not the manedit file, so edits probably get overwritten). I also have the feeling that we fixed something about the editing in longitudinal processing after 5.1, but cannot find it documented on the wiki (so not sure). You may want to try to run this with 5.3 if it does not work with 5.1 Best, Martin On 05/02/2014 10:45 AM, Douglas Merkitch wrote: Dear Freesurfer experts, I have a question regarding longitudinal edits. Specifically the brain.finalsurfs.manedit.mgz file and the longitudinal processing stream in Freesufer 5.1 on a Mac (freesurfer-i686-apple-darwin9.8.0-stable5-20110525). The problem that I am having is that the edits saved in the brain.finalsurfs.manedit.mgz file do not carry over when processing longitudinally. Previous posts have addressed this topic, but have not (to my knowledge) solved the issue. Please see the threads from the Freesurfer archive below for a brief context: 1. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27695.html 2. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33471.html Please let me know if more information is needed to understand the issue. Any insight/ideas regarding this issue would be greatly appreciated! Thanks, Doug Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Douglas_Merkitch(a)rush.edu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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TRACULA: ERROR in -qa Flag
by Shantanu Ghosh 13 Jun '14

13 Jun '14

Dear Anastasia and Freesurfer experts, I am trying to set up an analysis of motion parameters using the flag -q from a set of DTI Dicoms located on the Martinos cluster, but I am facing problems -- it says "ERROR: flag -qa unrecognized". My .tcshrc is set to Freesurfer5.3 and FSL. What am I doing wrong? My config file is attached and here are my commands. cd /autofs/space/glia_001/users/shantanu/dtistudy/ setenv PATH /usr/pubsw/packages/python/epd/bin:${PATH} setenv FSENV_KEEP_PROMPT setenv MNE_ROOT /usr/pubsw/packages/mne/stable setenv SUBJECTS_DIR /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons setenv FSL_DIR /usr/pubsw/packages/fsl/5.0.0 source /usr/local/freesurfer/nmr-stable53-env source /usr/pubsw/packages/mne/stable/bin/mne_setup ----My console output----- glia:shantanu[120] mynmr53 -------- freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons does not exist FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 FSFAST_HOME /usr/local/freesurfer/stable5_3_0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /autofs/space/calvin_001/marvin/1/users/MRI/WMA/recons MNI_DIR /usr/local/freesurfer/stable5_1_0/mni FSL_DIR /usr/pubsw/packages/fsl/5.0.0 MNE software location set to: /usr/pubsw/packages/mne/stable MATLAB software not available /usr/pubsw/packages/mne/stable/bin already in PATH /usr/pubsw/packages/mne/stable/lib added to LD_LIBRARY_PATH /usr/pubsw/packages/mne/stable/share/app-defaults/%N added to XUSERFILESEARCHPATH Note: Remember to set SUBJECTS_DIR and SUBJECT environment variables correctly. Note: FreeSurfer environment is needed to access tkmedit from mne_analyze. glia:shantanu[121] trac-all -qa -s 008801 -c /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt ERROR: flag -qa unrecognized -qa -s 008801 -c /autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt glia:shantanu[122] Thanks in advance for all help. Shantanu -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg

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