Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

UnicodeEncodeError while running the recon-all
by David Lau 27 Mar '23

27 Mar '23

External Email - Use Caution Hi, I tried to run Freesurfer (macOS-7.1.1) to the command line and the terminal replied, "DavidLaus-MacBook-Air:local davidlau$ recon-all -i /Users/davidlau/Desktop/testing/1RAS.nii -subject /Users/davidlau/Desktop/testing/$d done Traceback (most recent call last): File "/Users/davidlau/Documents/freesurfer/python/scripts/rca-config", line 143, in <module> file.write(arg + '\n') UnicodeEncodeError: 'utf-8' codec can't encode character '\udcc3' in position 0: surrogates not allowed ERROR: could not configure recon-all parameters" A similar question has been retrieved from the mail list (20 Jul 2020) by Molly and Andrew replied that there might be a non-unicode character accidentlly passed to the command line and recommended manually typing out the recon-all command. I've tried this several times but the same error message popped out. Any suggestions would be much appreciated. David

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mri_convert mosaic dicoms
by John Anderson 27 Mar '23

27 Mar '23

External Email - Use Caution Dear Dr Doug Greeve, For each participant in my dataset, I have 8 mosaic volumes with 36 slices each. I am trying to convert the DICOM files to Nifti format using the mri_convert command in FreeSurfer version 7.3.2. However, the conversion process fails even when using this latest dev version. To resolve this issue, I attempted to use the --nslices-override option. It seems working, however, I am unsure if I used it correctly, and I was not able to find any relevant examples or guidance on how to use this option in the FreeSurfer documentation or other websites. n=({-1..7}) unpacksdcmdir -src ./dicoms/ -targ ./ -scanonly log for i in $(cat dicomdir.sumfile | awk '{print $2}'); do n=$(($n + 1)) mri_convert ./dicoms/$i ASL_$n.nii -odt float --nslices-override 36 -f $n done Thanks for guidance, John

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Using the Desterieux Cortical Atlas to Extract PET SUVs
by Bues, Hannah Francesca 27 Mar '23

27 Mar '23

Good afternoon all, I was hoping to get some advice on how to approach this. Any and all feedback is much appreciated. My group has been using FSL’s Feat to run analyses for our PET-MR project. Part of what we need to do next is create masks using fslmaths that overlay the significant clusters in the zstat images with different brain regions. We then extract standard uptake values (SUVs) from the clusters in each region for each subject so that we can graph them. The issue is that the Atlas in FSL is the Harvard-Oxford Cortical Structural Atlas, which has a broader parcellation of the cingulate cortex then we would like to use (just anterior/posterior). Is there any way to use the Desterieux atlas with FSL? Or any way to do this same kind of analysis with Freesurfer? I would really appreciate the help. Best, Hannah -- Hannah Bues (she/her) Clinical Research Coordinator - VanElzakker Lab Martinos Center for Biomedical Imaging Massachusetts General Hospital/Harvard Medical School 149 13th Street, Charlestown, MA 02129 Office: (617) 726-8120

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mri_cvs_register cost function
by Federica Di Antonio 27 Mar '23

27 Mar '23

External Email - Use Caution Dear experts, May I ask you which cost function is used by mri_cvs_register? Thank you so much for your support! Federica Di Antonio

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Intracranial electrode visualization in Freeview
by Kerezoudis, Panagiotis, M.D., M.S. 27 Mar '23

27 Mar '23

External Email - Use Caution Hi, I have completed the Freesurfer segmentation and parcellation in a patient that has intracranial electrodes. I also have the electrode locations in various file formats (tsv, nii and pom). Is there a way to visualize their location in Freeview and particularly in 3D? For example, for 2D I can easily do that with microGL. Thank you very much in advance! Best, Panos Kerezoudis

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mri_glmfit error - matrix ill-conditioned. no solution from archive.
by miracle ozzoude 27 Mar '23

27 Mar '23

External Email - Use Caution Hello, Any idea how to solve this problem? I have tried the suggested solutions on the archive, that's Demean and Rescale but to no avail. I have attached the necessary files in the email below. Many thanks, Miracle mri_glmfit command: mri_glmfit --y results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh --fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf fsaverage lh --cortex --glmdir results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir

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cortical thickness and z-scores correlation
by Maria Czarnecka 27 Mar '23

27 Mar '23

External Email - Use Caution Dear Sisters and Brothers in neuroscience I am a huge fan but a very new user of the freesurfer, please treat me as such when answering this email. I have successfully performed anatomical and functional data analysis using fmriprep, freesurfer and fsfast. I have all the files needed, everything looks perfect. As a next step of my analysis I would like to perform a correlation of Cortical thickness and the functional activation in one of my contrasts (I would like to correlate the CT with the z-scores). I would like to do that separately for each subject and in ROIs (ideally, self-defined Rois, but if there is an easy way to do it in anatomical ones I will be very happy as well). What I need is for the program to take the z-score from each vertex in an ROI and the value of cortical thickness for each vertex and do the correlation on those values. I can also do the statistics in another tool (R), so simply extracting those values for vertices in an ROIs would be great. Do you have any suggestions how to do that? Best, Maria Czarnecka

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negative uptakes after GTM pvc correction
by Federica Di Antonio 27 Mar '23

27 Mar '23

External Email - Use Caution Dear experts, I report an answer you gave about some negative values avatar partial volume correction: "[...] Usually this only happens in small ROIs and/or low uptake regions. Why might the model not be perfect? It could be a number of things: 1. the MRI-PET registration is inaccurate 2. the MRI segmentation is inaccurate 3. the ideal segmentation is not reflected by the MRI segmentation (eg, one of the segmentations has a hot spot)" I wonder if it is possible for you to give me an hint about the reason why an inaccurate registration or segmentation can cause negative uptake values. At first sight it seemed intuitive to me, but on second thought that's not so obvious. I would be very grateful for any help! Federica Di Antonio

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mri_glmfit-sim error
by mariangela asimina 27 Mar '23

27 Mar '23

External Email - Use Caution Hello FreeSurfer developers and experts, I am trying to do cluster correction with mri_glmfit-sim after running mri_glmfit. The command I ran: mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs --cwp 0.05 --2spaces produces the following error: ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Operating System: Ubuntu 22.04.2 LTS Kernel: Linux 5.19.0-35-generic I have searched the archive and cannot find a similar error. I would appreciate your help. Mariangela Asimina I also ran the command with the --debug flag and I get the following output, but I'm afraid I can't interpret it: set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 8 != 0 ) set flag = $argv[1] ; shift ; set flag = --glmdir shift switch ( $flag ) switch ( --glmdir ) if ( $#argv < 0 ) goto arg1err ; if ( 7 < 0 ) goto arg1err set glmdir = $argv[1] ; shift ; set glmdir = lh.volume.SCNStudyTest.10.glmdir shift breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 ) set flag = $argv[1] ; shift ; set flag = --cache shift switch ( $flag ) switch ( --cache ) if ( $#argv < 2 ) goto arg2err ; if ( 5 < 2 ) goto arg2err set thresh = $argv[1] ; shift ; set thresh = 3.0 shift set simsign = $argv[1] ; shift ; set simsign = abs shift set UseCache = 1 ; set UseCache = 1 set DoSim = 0 ; set DoSim = 0 set thresh = `echo $thresh | sed 's/,/./g'` set thresh = `echo $thresh | sed 's/,/./g'` sed s/,/./g echo 3.0 set thresh = `printf %2.1f $thresh` set thresh = `printf %2.1f $thresh` printf %2.1f 3.0 if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && $thresh != 3.3 && $thresh != 4.0 ) then if ( 3,0 != 1.3 && 3,0 != 2.0 && 3,0 != 2.3 && 3,0 != 3.0 && 3,0 != 3.3 && 3,0 != 4.0 ) then echo "ERROR: thresh = $thresh, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0" echo ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 exit 1 ; exit 1

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head in a bad position in scanner
by Aaron Tanenbaum 27 Mar '23

27 Mar '23

External Email - Use Caution We acquired some data this morning where the participant's head was in an unusual orientation. The participant has cervical dystonia. I have processed data like this before and freesurfer always fails. I am assuming Freesurfer is unable to register the image. I have not even run this image through freesurfer yet. Is there a way to deal with this without altering the image?

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