Freesurfer July 2017

freesurfer@nmr.mgh.harvard.edu

118 participants
198 discussions

problem with bedpostx
by Lars M. Rimol 27 Jul '17

27 Jul '17

Hi, Running trac-all -bedp and getting an error message I've never seen before. I'm running it on a desktop, not a cluster, which it warns agains - but it should still run, shouldn't it? larsrim:~/lbkabel/tbi/morfometri_test$ trac-all -bedp -c DWI/jobscripts/d1_1001_local.dmrirc INFO: SUBJECTS_DIR is /home/larsrim/lbkabel/tbi/morfometri_test INFO: Diffusion root is /home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /home/larsrim/lbkabel/tbi/morfometri_test/DWI/TRACULA/local/1001_c1/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected Sincerely yours, Lars M. Rimol, PhD Senior Researcher Norwegian Advisory Unit for Functional MRI Department of Radiology St. Olav's University Hospital 7006 Trondheim Norway

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Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates
by Florence Campana 27 Jul '17

27 Jul '17

Hi Doug, Thank you for your reply. I computed the tkRAS coordinates using the formula TkRAS = Torig*[C R S 1]’. It returns me coordinates such as: [113, -119,88], [105, -103, 96]. I wonder whether such tkRAS coordinates are normal since in label files obtained by saving ROI upon a certain threshold in tksurfer, the coordinates seem fairly different: non integers, and in different ranges e.g. [-36.806 -18.293 64.462], [-21.393 -61.263 8.910]) etc. However, when I create a label file (via write_label.m) with -1 in the first column and with the TkRAS coordinates that I computed in the columns 2,3,4 , and then via tksurfer load this label and then save the selected label, I obtain a new label with R A S coordinates as [34.198 -48.599 29.835], [35.364 -45.689 31.179], i.e. similar to the one that I have in my ROI label files. Could you please help me to figure out what my tkRAS values (e.g.[113, -119,88], [105, -103, 96) correspond to, versus the ones returned by tksurfer ([34.198 -48.599 29.835], [35.364 -45.689 31.179])? I hope that it makes sense. Thank you so much! Florence *From:* Douglas Greve <greve(a)nmr.mgh.harvard.edu> *Date:* July 24, 2017 at 4:06:25 PM EDT *To:* <freesurfer(a)nmr.mgh.harvard.edu> *Subject:* *Re: [Freesurfer] converting vertex numbers in .label files to R, A, S coordinates* *Reply-To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Try using mri_label2label with the --paint option. I think the vertex numbers need to be -1 (not random numbers). You will also need to convert the RAS to "tkregisterRAS", one of our internal coordinate systems. See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems, you'll need to do the inverse of case #1. On 7/19/17 12:28 PM, Li Guo wrote: *Dear Freesurfer experts,* *My question concerns the .label files and the correspondence between the vertex numbers (in the first column) and the R,A,S coordinates.* *I have the R,A,S coordinates of voxels that I want to display on the surface. For this purpose, I created a label file with the R,A,S coordinates (col 2,3,4) and random vertex ID in the col 1 (since I do not know what is the vertex ID for a given R,A,S coordinate). I displayed the content of the label file via tksurfer. However, tksurfer reads vertex ID, not R,A,S coordinates. * *I wonder whether anyone knows about a function computing the vertex ID based on the R,A,S coordinates, or an alternative solution to represent the vertices on the surface based on the voxel coordinates--and the registration file I assume?* *Thank you very much!* *Best* *Li Guo & Florence Campana*

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Extract coordinates from .mgh file
by Redwan Maatoug 27 Jul '17

27 Jul '17

Hi experts, I just want to know a way to extract the coordinates from a ROI mgh file. I know that I can load the file with tksurfer but I have 100 .mgh files so if I could run a command line to have the coordinates in a .txt file or in a .m it would be helpful. Thank you, Redwan

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mri_glmfit --cortex flag
by Rockers, Elijah D. 27 Jul '17

27 Jul '17

From what I understand, the --cortex flag is simply supposed to zero out any signal in the medial wall with a mask, I checked mask.mgh, it is 0 on the medial wall and 1 everywhere else as expected... however when I analyze the data without this flag, the resulting sig.mgh file has completely changed. Areas on the cortex that were "lit up" disappear, and other areas light up that were silent before. This should not be happening right? Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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rh.white and rh.pial surface edit_Orbito-frontal Cort
by Farhad Ghaseminejad 26 Jul '17

26 Jul '17

Hello, I was wondering if you have any suggestions on how to fix the error in the rh.white and rh.pial surface in the Orbitofrontal cortex as shown in the screenshots attached. https://drive.google.com/drive/folders/0B64fNVlVdTBYOVhJMXJyTjZVSTQ?usp=sha… Best, Farhad

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MNI coordinates
by Redwan Maatoug 26 Jul '17

26 Jul '17

Hi all, My goal is to extract the coordinates from a .mgh ROI surface file. I have used this tool : mri_surfcluster with But the coordinates are in Tailarch and I would like the *MNI coordinates*. Someone has an idea ? Thank you, Redwan

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help with finding exact and detailed coordinates of brain areas
by עדיאל חרבש 26 Jul '17

26 Jul '17

Hi, I'm very new to Freesurfer, and actually work with some exist results of other people. The results are from the call of "-recon all -autorun". I try to get all the coordinates of each of the structures of the brain, that segmented. I can find on files only the volumes of some structures and something that look like detailed coordinates of Brodman Areas only. But I can't find the detailed coordinates of all structures in brain. I'll be grateful if someone can guide me where can I find it, or what should I do to get these results. Thanks, Adiel

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Clarification for aseg edits in longitudinal phase
by Tamara Tavares 26 Jul '17

26 Jul '17

Hello, I have made edits to aseg files in the longitudinal outputs (participantID.long.participantID-temp). I am beginning the reconstruction phase and as suggested by a response to an earlier post I am running: recon-all -long tpN1 template ID -autorecon2-noaseg -autorecon3, where tpN1 is cross-sectional output and template ID is the template of the participant. My questions are: 1) Does the script essentially take the edits I made in the aseg longitudinal outputs and reconstructs the longitudinal files using the cross and template files? 2) Does this script begin running recon-all during recon-all2, after the aseg files are suppose to be created? Thank you, Tamara

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Segmentation Violation problem in surface files
by Yagmur Ozdemir 19 25 Jul '17

25 Jul '17

Hello freesurfer experts, I am trying to use an occipital lobe template adapted to my data as several surface and volume files, and there seems to be a problem with the surface files. Whenever I try to open a surface overlay (in .mgz format) in freeview this error comes up; freadFloat: fread failed freadFloat: fread failed ... [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range ... When I try to convert this file to nifti format a seemingly similar error comes up; (...) mri_convert rh.template_areas.mgz AU_areas_template_rh.nii.gz mri_convert.bin rh.template_areas.mgz AU_areas_template_rh.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from rh.template_areas.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to AU_areas_template_rh.nii.gz... NIFTI FORMAT ERROR: nslices 117239 in volume exceeds 32768 I have tried to debug but failed so far. Has anyone come across a similar problem and do you have an opinion onto what might be causing this? The same adapted template's volume files work just fine. --I am using Ubuntu 16.04& freesurfer v.6 Thank you so much! Idil

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How to create mask for Total Graymatter and White matter Volume
by M Janani 25 Jul '17

25 Jul '17

Hi Team, I would like to create mask for Total Gray matter and white matter volume. I was able to get the total white matter volume using the below mentioned command mri_binarize -i aparc+aseg.mgz --wm --o wm.mgz But I couldn't find any option to create the mask for Total Gray matter. Any help would be really grateful. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

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Freesurfer July 2017