Freesurfer

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30055 discussions

recon-all-clinical rh.BA_exvivio.annot error
by Melissa Marie Rundle 11 Dec '24

11 Dec '24

External Email - Use Caution Hello, We are getting the error below for every subject when we run recon-all-clinical. It's only for the rh, not the lh. We are using Freesufer 7.4.1 with the synthseg python script. Let me know if there is a fix/update/patch for this. Thanks, Melissa ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt ERROR: cannot find or read /usr/local/freesurfer/dev/average/colortable_BA.txt computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /data/recon-all-clinical/3CAMC005746_125300857_20240220/mri/wm.mgz... reading input surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... reading input pial surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.pial... reading input white surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 183858 Total vertex volume 183685 (mask=0) error: No such file or directory error: could not read annot file ./rh.BA_exvivo.annot error: No such file or directory error: mris_anatomical_stats: could not read annotation file ./rh.BA_exvivo.annot computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /data/recon-all-clinical/3CAMC005746_125300857_20240220/mri/wm.mgz... reading input surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... reading input pial surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.pial... reading input white surface /data/recon-all-clinical/3CAMC005746_125300857_20240220/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 183858 Total vertex volume 183685 (mask=0) error: No such file or directory error: could not read annot file ./rh.BA_exvivo.thresh.annot error: No such file or directory error: mris_anatomical_stats: could not read annotation file ./rh.BA_exvivo.thresh.annot All done! ________________________________ This electronic message is intended only for the use of the individual(s) and entity named as recipients in the message. If you are not an intended recipient of this message, please notify the sender immediately and delete the material from any computer. Do not deliver, distribute or copy this message, and do not disclose its contents or take any action in reliance on the information it contains. Thank you.

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Re: [Freesurfer] Fwd: LME matrix design
by Diers, Kersten /DZNE 11 Dec '24

11 Dec '24

External Email - Use Caution Hi Daniel, please find my responses below. Hope this helps, Kersten External Email - Use Caution Hello FreeSurfer experts, I am currently working through the linear mixed effects pipeline to assess longitudinal cortical thickness changes in non-contact/contact athletes and have some questions. My design matrix is as follows: X = [ones(size(M,1), 1), M(:,1), M(:,2), M(:,3), M(:,1).*M(:,3), M(:,4), M(:,1).*M(:,4), M(:,5), M(:,6), M(:,7), M(:,8), M(:,9)]; M(:,1) = group M(:,2) = scan time from baseline M(:,3) = age With the rest of the columns in X being other covariates from M or *time interaction, and the random intercept term being the only random effect. 1. I’m using the spatiotemporal approach, but would vertex-wise yield more powerful results? I know that a previous thread had a similar question, but I am wondering if one would be more favourable for looking at regional CT changes. Hard to say, but I would not necessarily expect so, since the original paper demonstrated power increases for the spatiotemporal model as compared to the vertex-wise approach. 1. As well, the two groups have different distributions in timepoints and size. The contact athlete group is about double the size (42 vs 21) and has significantly more athletes with multi-year participation (2- or 3-years), whereas the non-contact athlete group is almost entirely single-year participation (one set of pre- and post-season scans). Is this something that the LME can inherently account for? Yes, the LME model can handle for designs with unbalanced number of cases, and differences in the number and interval lengths of longitudinal observations. 1. My main goal is to test if there is a significant difference in the slopes of the two groups (using lme_mass_F). I currently have this setup for my contrast matrix: CM.C = [0 1 zeros(1,10)]. Since I only have two groups, is it logical to use a single row? Additionally, I am a bit unsure of how to assign beta weights. Yes, using a single-row contrast like you say is fine. What exactly do you mean by "assign beta weights?" 1. After running the F-test, I am correcting the multiple comparisons using FDR2. Are there any other corrections/tests I should utilize before plotting data in tksurfer? You might want to take into account correcting for the fact that you are (likely) doing the analysis in two hemispheres: the tutorial suggests to simply do a bonferroni correction. Thank you in advance, Daniel The 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 https://secure-web.cisco.com/1spOb5VWb5CUeuy6CxGiwDR0ePXHBn09ABVNzN5LzwT8UJ… . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Re: [Freesurfer] Petsurfer: PET -> MNI305 problem
by Shen, Qian 10 Dec '24

10 Dec '24

External Email - Use Caution Hi Dr. Greve and Experts, I encountered an issue while running the following command to resample meltzer.nii.gz (or mgx.subctxgm.nii.gz) into the 2mm MNI305 space, as instructed in the PetSurfer wiki<https://secure-web.cisco.com/1W31n5cbq1zvsFiHcecMWmqEEiH13OUvfTH7j9X72O1Gdv…>. The output image appeared misoriented (see the attached screenshot for reference): mri_vol2vol --mov meltzer.nii.gz--reg aux/bbpet2anat.lta --tal --talres 2 --o meltzer.mni305.2mm.sm00.nii.gz Upon investigating, I realized the issue arises when using the --no-reduce-fov option in the mri_gtmpvc step. Specifically: (1)If I do not use --no-reduce-fov in mri_gtmpvc, the output image from above mri_vol2vol command is correct. (2)Alternatively, if I do use --no-reduce-fov, but replace aux/bbpet2anat.lta with either template.reg.lta or aux/anat2bbpet.lta in mri_vol2vol command, the output image is also correct. Could you confirm if this behavior is expected or if additional adjustments are needed? By the way, the version of Freesurfer I'm using is v7.1.0. Thank you for your guidance in advance, Shen

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Re: [Freesurfer] Error in longitudinal hippocampal fields
by Mark Wagshul 10 Dec '24

10 Dec '24

External Email - Use Caution This is a single case, all of my other subjects ran through without a problem. Thanks! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu<mailto:mark.wagshul@einsteinmed.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately. From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ(a)mgh.harvard.edu<mailto:JIGLESIASGONZALEZ@mgh.harvard.edu>> Subject: Re: [Freesurfer] Error in longitudinal hippocampal fields processing To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <PH0PR04MB83881AEB5CC0EDD5534404A2FD3C2(a)PH0PR04MB8388.namprd04.prod.outlook.com<mailto:PH0PR04MB83881AEB5CC0EDD5534404A2FD3C2@PH0PR04MB8388.namprd04.prod.outlook.com>> Content-Type: text/plain; charset="utf-8" ?Thanks for your message, Mark! Is this for a single case, or a more general issues? Cheers, /Eugenio

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Questions about CVS registration
by Tanxin Dong 10 Dec '24

10 Dec '24

External Email - Use Caution To whom this may concern: Hi, I’ve been working on creating a template for a certain metric using the applyMorph command to project the calculated metrics onto the CVS template. However, I'm curious if there’s a way to reverse this process. Specifically, can I morph the template in the CVS35 space back to the individual space? I would appreciate any insights or guidance you could provide on this. Looking forward to your response! Best regards T.D.

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Recon all across different image dimensions of different clinical subjects!
by JM 10 Dec '24

10 Dec '24

External Email - Use Caution Hi FreeSurfer experts, In our hospital research settings, we collected structural MRI data from patients while they were admitted for treatment. Some of the patients were scanned before contrast agent was injected and some were scanned after contrast agent was injected. There was no consistent protocol used. Some patients had 3D T1 data collected (with dimensions 512 x 512 x 248 with voxel size 0.47 x 0.47 x 0.7), some had Ax-T1 data (with dimensions 512 x 512 x 32 with voxel size 0.4 x 0.4 x 5) and some had only Sag-T1 data collected (with dimensions 256 x 256 x 25 with voxel size 0.85 x 0.85 x 6). Interestingly, recon-all works fine without any error across all three sets (i.e., 3D T1, Ax-T1 and Sag-T1). I would greatly appreciate your thoughts/suggestions/answers with the following: 1. Does it matter whether images are analyzed (i.e., recon-all 'd) on pre-contrast images or post-contrast images (in terms of output morphometry values [e.g., thickness, volume])? In other words, would it be OK if estimated pre-contrast morphometry values and estimated post-contrast morphometry values can further be analyzed in group level analysis OR subjects with pre-contrast can't be in the same group as subjects with post-contrast for further analysis (e.g., morphometry vs behavior values)? 2. Similarly, would it be OK if estimated 3D-T1 morphometry values and estimated Ax-T1 and Sag-T1 morphometry values can further be analyzed in group level analysis? Otherway, I was thinking was to resample the images to isotropic voxel size, then run recon all, and then combine subjects with 3D-T1, Ax-T1 and Sag-T1. OR subjects with 3D-T1 can't be in the same group as subjects with Ax-T1 and Sag-T1 for further analysis (e.g., morphometry vs behavior values)? In addition, any other suggestions on how I can utilize Ax-T1 and Sag-T1 data for morphometry analysis would be very helpful. I would greatly appreciate your response at your earliest convenience. Thanks!

2 1

Error in longitudinal hippocampal fields processing
by Mark Wagshul 09 Dec '24

09 Dec '24

External Email - Use Caution Hi, I'm running into an error running segmentHA_T1_long, it processes the left side just fine, but gives the following error and fails to produce the requisite output files for the right: "Unable to perform assignment because the left and right sides have a different number of elements." I've attached the log file, in case that helps in diagnosing the issue. Thanks! Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu<mailto:mark.wagshul@einsteinmed.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

2 1

Re: [Freesurfer] TRACULA error /bin/tcsh: bad interpreter: No such file or directory
by fsbuild 09 Dec '24

09 Dec '24

External Email - Use Caution Tcsh and other programs/files freesurfer uses are not installed by default on Ubuntu linux.  So to install fresurfer and also have the system install what freesurfer needs to run, you should use one of the freesurfer  .deb package installers available from,https://secure-web.cisco.com/1rgwwg0ZifTyCWJ3xhoWAUKZbDTEFuO5WZbY_1_dw…; To install the 7.4.1 release on Ubuntu 22, you would download,https://secure-web.cisco.com/1EZiIcgCiIUVcrk2eIaKVHB6rJya2cl1VbO03… On your machine you would change directories to where you downloaded that file and run the installer with the command,$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb That will install tcsh, other system files and install freesurfer under /usr/local/freesurfer/7.4.1.  Then you would set FREESURFER_HOME to /usr/local/freesurfer/7.4.1 and (re)set SUBJECTS_DIR to a path you can write to, e.g.,$ bash$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh… output deleted ...$ export SUBJECTS_DIR=$HOME/subjects$ mkdir -p $HOME/subjects - R. On Dec 9, 2024, at 11:39, Barletta, Valeria <VBARLETTA(a)mgh.harvard.edu> wrote:Hello Freesurfers, I am trying to launch trac-all -prep on Ubuntu 22 but I am getting this error: -bash: /home/local/PARTNERS/vb922/freesurfer/bin/trac-all: /bin/tcsh: bad interpreter: No such file or directory Can you please help me figure out what is going on? Thank you,Valeria_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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TRACULA error /bin/tcsh: bad interpreter: No such file or directory
by Barletta, Valeria 09 Dec '24

09 Dec '24

Hello Freesurfers, I am trying to launch trac-all -prep on Ubuntu 22 but I am getting this error: -bash: /home/local/PARTNERS/vb922/freesurfer/bin/trac-all: /bin/tcsh: bad interpreter: No such file or directory Can you please help me figure out what is going on? Thank you, Valeria

1 0

LME matrix design
by Bondi, Daniel 06 Dec '24

06 Dec '24

External Email - Use Caution Hello FreeSurfer experts, I am currently working through the linear mixed effects pipeline to assess longitudinal cortical thickness changes in non-contact/contact athletes and have some questions. My design matrix is as follows: X = [ones(size(M,1), 1), M(:,1), M(:,2), M(:,3), M(:,1).*M(:,3), M(:,4), M(:,1).*M(:,4), M(:,5), M(:,6), M(:,7), M(:,8), M(:,9)]; M(:,1) = group M(:,2) = scan time from baseline M(:,3) = age With the rest of the columns in X being other covariates from M or *time interaction, and the random intercept term being the only random effect. 1. I'm using the spatiotemporal approach, but would vertex-wise yield more powerful results? I know that a previous thread had a similar question, but I am wondering if one would be more favourable for looking at regional CT changes. 2. As well, the two groups have different distributions in timepoints and size. The contact athlete group is about double the size (42 vs 21) and has significantly more athletes with multi-year participation (2- or 3-years), whereas the non-contact athlete group is almost entirely single-year participation (one set of pre- and post-season scans). Is this something that the LME can inherently account for? 3. My main goal is to test if there is a significant difference in the slopes of the two groups (using lme_mass_F). I currently have this setup for my contrast matrix: CM.C = [0 1 zeros(1,10)]. Since I only have two groups, is it logical to use a single row? Additionally, I am a bit unsure of how to assign beta weights. 4. After running the F-test, I am correcting the multiple comparisons using FDR2. Are there any other corrections/tests I should utilize before plotting data in tksurfer? Thank you in advance, Daniel

1 0

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