Freesurfer

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30088 discussions

Errors when visually inspecting aseg.mgz
by Maria-Eleni Dounavi 14 Mar '19

14 Mar '19

External Email - Use Caution Dear Freesurfer developers and users, I am running the freesurfer recon-all pipeline for a big dataset and I am particularly interested in the hippocampus. For 20% of my subjects the hippocampus along with other subcortical structures are misplaced in the aseg.mgz image, which affects also the subsequent subfield analysis. ? I was wondering which steps must be followed to fix this and which surfaces need to be corrected. So far I have corrected/checked the initial brain mask and added control points to the analysis but there is no difference in the end result. I would be grateful if you could let me know how to tackle this issue. Apologies if a similar question has been asked in the past and I missed it. Best Wishes, Marialena

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recon-all to fsaverage
by Laboratorio de Neurociencia Funcional 14 Mar '19

14 Mar '19

External Email - Use Caution Dear Freesurfers, I would like to apply recon-all to the fsaverage subject of my sample to get all the labels that are obtained in each individual subject. However, it is not possible because my average subject doesn't contain the file /orig/001.mgz required to run the recon-all. Could you help me to handle this issue? Many thanks in advance. Best regards, Jose

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ROI mask extraction from asec and apark
by Tim Hahn 14 Mar '19

14 Mar '19

External Email - Use Caution Dear Freesurfer experts, as far as I understand, Freesurfer employs the Desikan-Killiany Atlas (by default) to compute the various parameters based on the aseg and aparc files. For my analysis, I now need the Desikan-Killiany Atlas ROI mask(s) (cortical and subcortical) in MNI or Talairach space. Is there any way to obtain these masks, e.g. by converting aseg/aparc files or by downloading them somewhere? Thanks a lot for your help. Best, Tim

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recon-all: making sure that brain.mgz will be in RAS orientation.
by Peled, Noam 14 Mar '19

14 Mar '19

Dear group, I ran recon-all on a T1 nii file, which is in LAS orientation. The brain.mgz turn out to be in LIA orientation. I've tried to convert the nii file to RAS (mri_convert --in_orientation LAS --out_orientation RAS ...), and rerun recon-all, but it didn't change the results. How do I make sure my output files will be in RAS orientation? Thanks, Noam

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Re: [Freesurfer] Welch's t-test for HOV violation
by Hannah CK 14 Mar '19

14 Mar '19

External Email - Use Caution Hi Dr. Greve, Sorry about that - I had followed the "Reply via email" link on the archive page instead of posting to the forum directly. Thank you for this response. Can extracting the means be done at the whole-brain level? If we get the means and variances for each group, I'm assuming we would need to use ROIs. Could you please clarify whether it's possible to extract means across the whole brain? Thank you, Hannah Re: [Freesurfer] Welch's t-test for HOV violation 2019-03-13 Thread Greve, Douglas N.,Ph.D. Hi Hannah, please include the previous correspondence so that we have context. Also, please remember to post to the list and not to us personally. thanks! doug On 3/13/19 10:52 PM, Hannah CK wrote: External Email - Use Caution Hi Dr. Greve, Thank you for this response. Can extracting the means be done at the whole-brain level? If we get the means and variances for each group, I'm assuming we would need to use ROIs. Could you please clarify whether it's possible to extract means across the whole brain? Thank you, Hannah ___ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Re: [Freesurfer] Welch's t-test for HOV violation 2019-03-11 Thread Greve, Douglas N.,Ph.D. I used to have this about 20 years ago, but I stopped supporting it when it did not fit cleanly into the GLM ... The shortest route is probably to do two separate analyses with mri_glmfit, one for each group. This will output means and variances for each group. Then use fscalc to compute maps of the Welch's t. On 3/11/19 1:28 PM, Hannah CK wrote: > > External Email - Use Caution > > We are conducting t-test comparisons across groups in which there is a > large discrepancy in group sizes. HOV is violated. I've searched for > ways to run Welch's t-test in FreeSurfer (or a similar analysis that > does not assume homogeneity of variance) but am not finding one. > > Could anyone please advise on how to do this? > > Thank you.

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Error with mri_label2label(Segmentation fault(core dumped))
by 310913949 14 Mar '19

14 Mar '19

External Email - Use Caution Hi Bruce, I drawed a 3D ROI on the original image using freeview,and saved it as an label file. Then I wanted to sample it to my subject and to found the closest surface vertices so that I can extract the cortical thickness of ROI. I used the command line: mri_label2label --srclabel 4gt.label --s PT1_4 --trglabel 4reg.on-pial.label --hemi rh --paint 30 pial --trgsurf pial. But it reported error: Line 3:4445 Segmentation fault(core dumped), mri_label2label.bin "$@". Can you tell me how to solve this problem?Is it wrong to use the mri_label2label? Thanks. Best wishes， Kan Deng

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Re: [Freesurfer] Welch's t-test for HOV violation
by Greve, Douglas N.,Ph.D. 13 Mar '19

13 Mar '19

Hi Hannah, please include the previous correspondence so that we have context. Also, please remember to post to the list and not to us personally. thanks! doug On 3/13/19 10:52 PM, Hannah CK wrote: External Email - Use Caution Hi Dr. Greve, Thank you for this response. Can extracting the means be done at the whole-brain level? If we get the means and variances for each group, I'm assuming we would need to use ROIs. Could you please clarify whether it's possible to extract means across the whole brain? Thank you, Hannah

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subcortical segmentation
by Sanchez, Juan (NYSPI) 13 Mar '19

13 Mar '19

External Email - Use Caution Dear Freesurfer community, Our group is using the new FreeSurfer 6.0 (dev) subcortical segmentation scripts on HCP data (Freesurfer 5.3) segmentHA_T2.sh segmentThalamicNuclei.sh We have successfully segmented the three structures 1. lh.hippoAmygLabels-T1-T2_seg.v21.mgz 2. rh.hippoAmygLabels-T1-T2_seg.v21.mgz 3. ThalamicNuclei.v10.T1.mgz We have found that there is significant overlap (see attached) bilateraly at the tail of the hippocampus. This makes some sense anatomically but we need to define these areas as a unique structure. Has anyone dealt with this overlap ROI issue before? Thanks Juan Sanchez - Pena

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Thalamic nuclei longitudinal analysis
by Antti Cajanus 13 Mar '19

13 Mar '19

External Email - Use Caution Dear FS experts, I'm using the thalamic nuclei segmentation on T1-images. Is it possible to perform longitudinal analysis with this data, or could I just segment the different time points separately to see volume reduction of specific nuclei? Best, Antti Cajanus PhD student

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'mghRead -1 error: could not open file' when running mri_info from Matlab
by Suzanne Witt 12 Mar '19

12 Mar '19

External Email - Use Caution Dear all, I have a matlab script that includes the following call to freesurfer: [status, result] = system(‘mri_info fsaverage/mri/brain.mgz —vox2ras-tkr'); The matlab script errors out at this step with the following output: status = 1 result = ‘mghRead(fsaverage/mri/brain.mgz, -1): could not open file’ If I run the mri_info command on the exact same file outside of matlab, I get the correct 4x4 matrix as output. I am running freesurfer 5.3.0 and matlab 2018b on a HPC system. I think I have all of the necessary paths for freesurfer set correctly in my matlab startup.m file: freesurfer/bin freesurfer/fsfast/bin freesurfer/mni/bin I am not sure why mri_info is giving correct input when run from the bash terminal prompt but throws this mghRead error when attempting to run the same command through matlab. The matlab script itself works on the mac desktop computer of the author (not sure what version of freesurfer or matlab the author is running), so the problem does not appear to be with the matlab system call to mri_info per se. Any suggestions of what else to troubleshoot (or if I am missing any path specifications in my startup.m file) would be much appreciated. For completeness, below is the output from ‘source $FREESURFER_HOME/SetUpFreeSurfer.sh’: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0<http://soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0> FSFAST_HOME /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/fsfast<http://soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/…> FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/subjects<http://soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/…> MNI_DIR /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/mni<http://soft.computecanada.ca/easybuild/software/2017/Core/freesurfer/5.3.0/…> Thanks, suzanne [cid:67412C66-BB70-409C-BE50-7BADCECDE5F9@uwo-x-11.wireless.uwo.pri]

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