Freesurfer July 2022

freesurfer@nmr.mgh.harvard.edu

90 participants
122 discussions

etiv value differs if using recon all vs freesurfer dev
by Miriam Taza 28 Jul '22

28 Jul '22

External Email - Use Caution Hello, I am getting different etiv values when running recon(orange) all VS mri_sclimbic_seg (blue). My analysis uses limbic volumes extracted from the dev version but I am not sure if I should just use the etiv from recon all, given the data is tighter (see attached). Why is there this discrepancy and what do you recommend? [cid:37ebf2b4-95b9-4b28-8fe6-86715ee89d72] Thank you!

2 8

Re: [Freesurfer] Cortical Thickness measures using different ways of processing
by Ariana Fei 28 Jul '22

28 Jul '22

External Email - Use Caution I'm attaching a list of command I used to convert freesurfer cortical thickness output to native space: $Caret5_Command -file-convert -fsc2c "$FreeSurferFolder"/surf/"$hemisphere"h.thickness "$FreeSurferFolder"/surf/"$hemisphere"h.white "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii $Caret5_Command -spec-file-add "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".native.c5.spec surface_shape_file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii $Caret5_Command -metric-set-column-name "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii 1 "$Subject"_"$Hemisphere"_Thickness $Caret5_Command -file-convert -format-convert XML_BASE64 "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii $Caret7_Command -set-structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii $Structure $Caret7_Command -add-to-spec-file "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii $Caret7_Command -metric-palette "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii MODE_AUTO_SCALE_PERCENTAGE -pos-percent 2 98 -palette-name Gray_Interp -disp-pos true -disp-neg true -disp-zero true #cp "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii #commented out GW $Caret7_Command -add-to-spec-file "$T1wFolder"/"$NativeFolder"/"$Subject".native.wb.spec $Structure "$T1wFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".thickness.native.shape.gii This already gives negative cortical thickness values in native space. Ariana

2 1

Unsubscribe?
by Archibald, Jessica 28 Jul '22

28 Jul '22

External Email - Use Caution Hi, I signed up last night to send a freesurfer question, but I figured it out. Now I am getting bombarded with emails from this thread and can’t see a ‘unsubscribe’ button. Can you help with this?? Thanks in advance, Jessica Jessica Archibald M.Sc. Kramer Lab- PhD candidate Experimental Medicine ICORD | Blusson Spinal Cord Center 818 W 10th Ave Vancouver, BC, Canada. [UBC E-mail Signature]

2 1

Help with improving the training of an alternative atlas for medial temporal lobe subregions
by Henzen Nicolas 28 Jul '22

28 Jul '22

External Email - Use Caution Hi all, We are aiming at training an alternative atlas of some subregions in the medial temporal lobe using FreeSurfer. As training examples, we manually segmented the subregions using tkmedit and tksurf. In this process we deleted the original segmentation labels around our new regions of interest (see Figure 1). Then, we trained the atlas and parcellated new data as follows: # Train atlases for hemi in lh rh; do mris_ca_train -n 2 \ -t ./doc/LUT.txt \ ${hemi} \ sphere.reg \ CUSTOM_ROIs.annot \ S01 S02 S03 S04 S05 S06 \ ./atlas/${hemi}.CUSTOM_ROIs.gcs done # Create annotations for hemi in lh rh; do for ID in S10 S11 S12 S13; do mris_ca_label \ -orig white \ -novar \ -t doc/ LUT.txt \ ${ID} \ ${hemi} \ sphere.reg \ ${hemi}.CUSTOM_ROIs.gcs \ $SUBJECTS_DIR/${ID}/label/${hemi}.CUSTOM_ROIs.annot done done [cid:image001.png@01D89C87.200FE420]This lead to a very inaccurate parcellation (see Figure 2), also when we filled the unlabeled region with a dummy label (see Figure 3). Figure 1. Example for manual segmentation of the 4 subregions (encircled) with deleted original segmentation labels around. [cid:image003.png@01D8A190.FBE5BED0] Figure 2. Parcellation example using the trained atlas without dummy label for unlabeled regions. [cid:image006.png@01D8A192.42B1DF00] Figure 3. Parcellation example using the trained atlas with dummy label for unlabeled regions. Any comments or suggestions on how to deal with our problem would be greatly appreciated. Many thanks for having taken the time to read and reflect Best, Nicolas

3 2

Cortical Thickness measures using different ways of processing
by Ariana Fei 28 Jul '22

28 Jul '22

External Email - Use Caution Hi, We are recently trying to get cortical thickness from freesurfer and converting them to 32k. A problem we notice is that after converting to 32k, all the cortical thickness values become negative. However, when we load freesurfer thickness files in freeview, everything appears normal. We wonder if merely inverting what we currently have in 32k would be a good idea. Alternatively, we also calculated the Euclidean distance of pial and white after they have been converted into 32k space, which should be cortical thickness. However, when comparing the inverted values and the "pial-white"values, we find that there are some differences. In this case, has anyone ever had similar issues and have suggestions on which one to trust? Thanks! Ariana

2 1

Applying bonferroni clusterwise correction for 2spaces with PALM F-contrast
by Hye Min Shin 28 Jul '22

28 Jul '22

External Email - Use Caution Hello experts, I am going through FreeSurfer's repeated measures anova tutorial using fspalm. I understand that fspalm frontend can only do t-tests at the moment and NOT F tests as noted in this thread: https://secure-web.cisco.com/1t11cJOK6FCdHxqm_O6WFHk15uAjWyctjoR7VAvgTW5hEa… So I am trying to run F-contrast on PALM but I was wondering if I also have to worry about bonferroni clusterwise correction. If I used --2spaces option when using fspalm frontend, I thought I should also try to apply the equivalent bonferroni correction when running F-test on FSL palm. For the F-test on FSL palm, it looked like I could run the following command with the addition of -f and -ftestonly flags (shown in underline): palm -i lh.thickness.mgz -i rh.thickness.mgz -d design.mat -t design.con *-f design.fts* -o myresults -n 2000 -corrcon -corrmod *-ftestonly* taken from this email thread- https://secure-web.cisco.com/1vFEFTKkUMsHsCHW3u3SsOIpxhqtkKCXdjWw6TLTufecii… Would this be equivalent to the bonferroni correction methods that fspalm uses? When I go through fspalm.log it seemed to run mri_surfcluster and mri_segstats after running fspalm with certain commands having --sig2p-max and --bonferroni-max 2 flags. Thank you in advance for your help! Best, Julia Shin

1 0

mri_jacobian questions
by Danielle Carrol 27 Jul '22

27 Jul '22

External Email - Use Caution Hello Freesurfer experts! I have been trying to send this question a few times, but it has never shown up on the archive, so I'm not sure if it has been received. I apologize if everyone has been receiving the same question multiple times! I am trying to compute the Jacobian for use in VBM. I found the following command on this email archive (Re: [Freesurfer] Jacobian mri_cvs_register (mail-archive.com) <https://secure-web.cisco.com/1PxtNE3QwqzX1SDyVeD_p5OwDGQgLiBBekceqUimQr0kRg…>: mri_jacobian <3d morph> <template volume> <output volume> I am assuming the 3d morph is the file mri/transforms/talairach.m3z, which is created during recon-all, since this file provides the nonlinear warp. However, I am confused about which file should be the “template volume”. Is this the final transformed/registered volume for each subject: ${SUBJECTS_DIR}/<subject name>/mri/brain.mgz)? Is it the fsaverage MNI template: $FREESURFER_HOME/subjects/fsaverage/mri/mni305.cor.mgz? I also thought it could be this file: freesurfer-latest/average/RB_all_2016-05-10.vc700.gca since I saw on the wiki page for recon-all that in the creation of the .m3z morph file, the nonlinear transform is computed to align with the GCA atlas, so that could be the "template" (recon-all - Free Surfer Wiki (harvard.edu) <https://secure-web.cisco.com/1dWy6gXJGfzUBSGAO9bR9NM58WNn9B3AwqHd2Y8dt6SwTh…> ). I am using version 6.0.0. Thank you for you advice and time, Danielle PhD Student University of Wisconsin-Madison

3 3

ERROR: Talairach failed
by Bouchra Guelib 27 Jul '22

27 Jul '22

External Email - Use Caution I have a nifty MRI, converted to mni 305 space when I apply recon-all, I have this error: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0525, pval=0.0034 < threshold=0.0050) Command exited with non-zero status 1 @#@FSTIME 2022:07:22:11:11:46 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M 6628 F 0 R 266 W 0 c 0 w 1 I 0 O 0 L 2.89 2.56 1.45 @#@FSLOADPOST 2022:07:22:11:11:46 talairach_afd N 4 2.89 2.56 1.45 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. see http://secure-web.cisco.com/11upxJF_-cI-E4FBY17KCMERFQk_Wf_2bOtw3CCmUNLSGGV… ERROR: Talairach failed! what should I do? -- *GUELIB Bouchra: *Ph.D. student *Lire *Laboratory University: Constantine 2-Abdelhamid Mehri- *Algeria * Alternative email: Guelibbouchra(a)gmail.com

2 4

TRACULA -bedp parallel processing
by Salar Dini, Elaheh 27 Jul '22

27 Jul '22

External Email - Use Caution Hello, I have tried to create a text file with command lines that can be run in parallel by using trac-all -bedp -c <config file> -jobs Parallel. When I use this command three text files are produced named: pre.Parallel, post.Parallel, and Parallel. Should I just use Parallel as a source for command lines? What are pre.Parallel and post.Parallel for? I am attaching my Configuration file, pre.Parallel, post.Parallel, and Parallel to this message as well. OS: Centos 7, Freesurfer version: 7.2.0 Thank you for your help. Kindly, Ela

4 14

Understanding ?h.sphere.reg
by Salar Dini, Elaheh 27 Jul '22

27 Jul '22

External Email - Use Caution Dear freesurfer experts, I was wondering if ?h.sphere.reg files have any coordinates in space tagged to them? What I actually mean is I'm using TRACULA which itself use the following files from mri and surf folder (all created by running recon-all on T1 image): aparc+aseg.mgz, brain.mgz, brainmask.mgz, orig.mg, T1.mgz and ThalamicNuclei.v12.Ta.FSvoxelSpace.mgzlh.thickness,rh.thickness,lh.white,rh.white,lh.sphere.reg,rh.shere.reg. I have all these files (except ?h.thickness and ?h.sphere.reg) in new coordinates in space created by co-registration. The pipeline we use to create recon-all results is almost the same as freesurfer pipeline with a slight difference in autorecon1 step, so the final results are almost always the same but the coordinate of the brain in 3D space is different, so we usually end up co-register one's reconstruction result (from our pipeline) with oneself T1.nii (come from mri_convert T1.dcm) so the structural mri reconstruction and dwi dcm files are in the same coordinate and can overlay. My understanding is that there is no coordinate tagged to ?h.sphere.reg files in 3D space, rather they are regulatory files which include some information about x,y,z vertices in regard to the surface of a hypothetical sphere (and the xyz are coming from the curvature of one's brain). As a result, I can use ?h.sphere.reg files as they are without any need to make any changes to match my files after they are coregistered. Is my understanding correct? I'm sorry if my language is not clear enough. I tried my best to describe the situation, but I'm not sure if my description is clear enough. Thank you for your help and time. Ela

2 4

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer July 2022