Freesurfer July 2023

freesurfer@nmr.mgh.harvard.edu

93 participants
130 discussions

conjunction analysis stats
by Maria Czarnecka 20 Jul '23

20 Jul '23

External Email - Use Caution Dear Sisters and Brothers in neuroscience, I have a problem with conjunction analysis. I do my analysis using: *mri_concat --i con1/sig.nii.gz --i con2/sig.nii.gz --min --o con.nii.gz* I get a nice map, there are clusters. What about the multiple comparison correction? Maybe I should do the conjunction on the already corrected maps? I would also like to get the cluster table for this conjunction. I tried: mri_surfcluster and it gives me Found 0 clusters and does not save anything. I will be grateful if you help me find the problem. Kind regards, Maria Czarnecka

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Re: [Freesurfer] Pial and White surface maps are not found
by fsbuild 20 Jul '23

20 Jul '23

External Email - Use Caution  Hello Varun, The Windows file system, i.e., NTFS, does not support soft links.  So you cannot set SUBJECTS_DIR to storage mounted from your Windows machine that has been formatted by Windows OS, and then run something in the linux VM that is going to try to write and create a soft link there, e.g., if that is what /media/sf_VBOX/T1_FreeSurfer is set to point to via SUBJECTS_DIR.   Anything that writes and creates a soft link running in the linux VM needs to write directly to the linux file system inside the VM. - R. On Jun 21, 2023, at 11:55, Varun Chandran <varunchandran28(a)gmail.com> wrote:        External Email - Use Caution        p.s. I am wondering whether this specific issue arises while working with freesurfer using Linux based Virtual Machine? On Wed, Jun 21, 2023 at 4:47 PM Varun Chandran <varunchandran28(a)gmail.com> wrote:Hi  YujingThank you very much for your quick reply. Yes, I used a directory path to set an environment variable (SUBJECTS_DIR=/media/sf_VBOX/T1_FreeSurfer) before running the 'recon-all' command line. However, it was not very helpful to obtain the pial and white surface maps and exited with some errors as shown in the recon-all.log (please see the file attached). Now, I'll try running the same command by entering the full path name of the directory as you suggested.                                                                                                                                 thanks again,best,VarunOn Wed, Jun 21, 2023 at 4:13 PM Huang, Yujing <YHUANG43(a)mgh.harvard.edu> wrote:        External Email - Use Caution        Hi Varun, I’m not sure what issue that you have been running into. Can you send your recon-all.log? In general, you need to1. set environment variable SUBJECTS_DIR to some directory that you have write permission2. pass full path to T1 image to -i <full_path_to_T1_image> Best, Yujing  From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Varun ChandranSent: Wednesday, June 21, 2023 10:32 AMTo: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] Pial and White surface maps are not found         External Email - Use Caution        Hi FS experts, It's been a few years, I used FS tools for cortical surface reconstruction. Now, when I used the freesurfer 7.2 version to perform cortical surface reconstruction on the T1-weighted structural MRI data, I was unable to obtain the lh/rh.pial and lh/rh.white surface maps. Can anyone please shed some light on this issue? command line used: recon-all -s T1_260423 -i T1_260423 -all -qcache                                                              thanks, best,Varun -- Varun Arunachalam Chandran, PhDPostdoctoral Research Associate,Faculty of biology, medicine and health,School of health sciences,University of Manchester,United Kingdom.MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1paAi-ZpIjFc28BcfldAkIvpne_JXV1wSSTxNf… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZXw_kqqZ3KZ69Di0XOLR2y7cRSFo0QTVxLkue… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1oLoAtw1TpZh6szgfCA5qRM4stI7vUsPUnYCur…; .-- Varun Arunachalam Chandran, PhDPostdoctoral Research Associate,Faculty of biology, medicine and health,School of health sciences,University of Manchester,United Kingdom.MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1i4aoGzHc6a0AY8hqw5Q4UmY5qB-iVj7FH4bDe… Arunachalam Chandran, PhDPostdoctoral Research Associate,Faculty of biology, medicine and health,School of health sciences,University of Manchester,United Kingdom.MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1paAi-ZpIjFc28BcfldAkIvpne_JXV1wSSTxNf… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_segstats dimension mistach
by Fahad Hannan 20 Jul '23

20 Jul '23

External Email - Use Caution Hello, I'm trying to run the mri_segstats on different input volume. The input volume has the same dimensions as the original volume used to perform recon-all. However, when trying to use the following command: "mri_segstats --seg $SUBJECTS_DIR/P6V1/mri/wmparc.mgz --sum $SUBJECTS_DIR/P6V1/stats/T2lobestest.stats --id 3201 4201 3203 4203 3204 4204 3205 4205 3206 4206 3207 4207 --in T2_Map.nii.gz --in-intensity-name norm --in-intensity-units MR --etiv --subject P6V1 --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt" I get a dimension mismatch error: ERROR: dimension mismatch between input volume and seg input 112 112 80 seg 256 256 256 Seems like during the recon-all process, freesurfer changed the dimensions of the segmentation file to 256 256 256. Is there a way I can resample the segmentation file to the input files dimensions, I know I can resample the input to the norm.mgz file but I do not want to tamper with the input file. Thanks, Fahad

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Problem accessing Buckner40 dataset
by vinuyan sivakolunthu 20 Jul '23

20 Jul '23

External Email - Use Caution Hello Freesurfers, I was trying to access the Buckner40 dataset. There is a fswiki page (https://secure-web.cisco.com/1ErZy9Sg7G0YZ9UZZX83Rz-_dcAsmHYvah0YuvSE1eQCjA…) that points to http://secure-web.cisco.com/1pATPjOdSJnK9tKEHQFm0-GAYffJ_TPyPC3Y39dGCwhvYhQ…, but the site is no longer up. Is there somewhere else where I could obtain the data? Thanks, Vin

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Some bugs in FreeSurfer 7.2.0
by 周乐晴 20 Jul '23

20 Jul '23

External Email - Use Caution Dear Sir, I can find Visual_v3_d cortex area in FreeSurferColorLUT.txt.  but I was confused that where I can find the result file of the visual cortex, or it needs more process?                                                                         Sincerely                                                                        Rosie Zhou  

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free surfer gets stuck during recon-all
by Rona Haker 20 Jul '23

20 Jul '23

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to do a full brain segmentation for a subject in my study using recon-all but after hours of running it did not reach the final step of creating aparc+aseg (the file I need), even though no error was printed. The last file that was created was 14 hours ago (till I stopped the run manually just now). my command is: recon-all -s ./00_FSseg -i ./8_t1_mp2rage_sag_p3_iso_UNI_Images/004933_t1_mp2rage_sag_p3_iso_UNI_Images_1.dcm -openmp 8 -all Attached is the log report of the run. By the way, this is a subject I have tried 3 times already to segment with no success, although most subjects in my study succeeded on the first try. recon-all -version command outputs this: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Thank you, Rona Haker

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ill conditioned matrix
by 조상아 20 Jul '23

20 Jul '23

External Email - Use Caution I attached fsgd, matrix and error captured file I don't know why this error occurs.

2 1

Asymmetry analysis
by Carlos Alcocer 20 Jul '23

20 Jul '23

External Email - Use Caution Hello, I am trying to do an asymmetry analysis using steps detailed in https://secure-web.cisco.com/1E9BKFPFixB_mpRwvgfFNlEN0qYfJdo8MVLo6aeqDf-afy… However, step 1.3 starts with running: mris_apply_reg --src lh.map.mgh --trg lh.map.lh.fsaverage_sym.mgh --streg $SUBJECTS_DIR/subject/surf/lh.fsaverage_sym.sphere.reg $FREESURFER_HOME/subjects/fsaverage_sym/surf/lh.sphere.reg What is this lh.map.mgh file? and where can I find it/how can i make it? Thank you, Carlos

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Extracting cortical thickness values for each subject using labels
by Akansha Mahesh Naraindas 20 Jul '23

20 Jul '23

External Email - Use Caution Hi I have made custom labels to use as ROIs, I was wondering if there was any way to get thickness values at each vertex for a participant but just within the areas covered by specific label files, So from the lh.thickness.fwhm0.fsaverage.mgh file, would I be able to extract thickness values from this file, but just within the region covered by aparc-rh-046.label ? Do you know of a way to do this? Thanks Akansha

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Fwd: error in recon all
by alanood alsaleh 20 Jul '23

20 Jul '23

External Email - Use Caution Hello Freesurfer developer I tried to run a recon all commands for 36 subjects, and 30 finished without any issues. However, 6 of them were terminated with the ERROR (Talairach failed!). Can you please help me to sort this problem out? Please find the attachments (I attached the recon all script I used and the log file that I got for the subject with an error ). Regards Alanood

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Freesurfer July 2023