[Freesurfer] MP2RAGE recon-all

External Email - Use Caution Dear Freesurfer experts: I am having trouble processing with recon-all the file I obtain with presurfer from an MP2RAGE. I don’t know if you have any experience with this. The data I obtained from this https://secure-web.cisco.com/1DoAeFvUHnYto_t5xo

Re: [Freesurfer] lh.pial lh.pialT1n same file?

of Douglas N. Greve Sent: Thursday, December 22, 2022 11:59 AM To: Huang, Yujing ; Renew Andrade ; Dicamillo, Robert Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] lh.pial lh.pialT1n same file?   yes, you can copy that. I'm cc'ing Rob in case he has any insights. @

Re: [Freesurfer] lh.pial lh.pialT1n same file?

recon-all log. > > I’m wondering if ‘ln -sf’ works on Mac. > > Can you try the following: > 1. cd to ‘surf’ directory > 2. ln -sf lh.pial.T1 testlink > 3. ls -l testlink > 4. ls -lt ?h.pial* ?h.white* ?h*.sphere.reg > > Can you send the output from tho

Re: [Freesurfer] lh.pial lh.pialT1n same file?

-Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Renew Andrade Sent: Tuesday, December 13, 2022 7:24 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] lh.pial lh.pialT1n same file? External Email - Use Caution Dear experts: I am

[Freesurfer] lh.pial lh.pialT1n same file?

External Email - Use Caution Dear experts: I am wondering if lh.pial and lh.pialT1 are the same files. I don’t have lh.pial is that an error from recon-all? Should I rerun recon-all. Or just autorecon-pial? Would that change anything? Best, Rene Andrade.

[Freesurfer] Medial wall mask for FSL tractography

External Email - Use Caution Dear experts: I have a doubt about finding the medial wall mask of a subject. Would this be ok? mri_label2label --srclabel lh.cortex.label --trglabel lh.cortex.label --outmask lh.cortex.mask.nii.gz --regmethod surface --hemi lh --srcsubject 25633

Re: [Freesurfer] format bvalues bvectors tracula

External Email - Use Caution Dear Yendiki Anastasia: I am replying for second time. I haven’t received an answer about this issue. I don’t know if it is silly but I don’t know how to fix it. It is not / slashes in this case. dmrirc.IXI Description: Binary data Sincerely,

[Freesurfer] tracula error too many ('s

External Email - Use Caution Dear FreeSurfer experts: I mentioned an error that I still cannot fix. I don’t think is the “\” because as you can see in the file attached everything seems correct. I cannot fix the issue with TRACULA I attach the configuration file so you can check

[Freesurfer] Functional connectivity analysis ERROR: cannot find.../dof

External Email - Use Caution Dear FreeSurfer experts: I cannot fix the problem that I mention in the subject. I put the output of the terminal below. I was doing functional connectivity analysis walkthrough tutorial and I followed until group analysis when applying "isxconcat-ses

[Freesurfer] study design flair T1

External Email - Use Caution Dear FreeSurfer experts: I am dealing with a crossectional retrospective case control study where I don't have all subjects with the same inaging protocols. I do have T1 for all of them although some have T2 others FLAIR others T2+FLAIR (besides T1

[Freesurfer] format bvalues bvectors tracula

External Email - Use Caution Dear FreeSurfer experts:I have tried to run tracula -prep but I cannot get to no where for the moment. I keep receiving this error. I assumed numbers had to be aligned in rows and columns. But none either that or one space in between seems to work. I

[Freesurfer] tracula error gradient vectors too many ('s

External Email - Use Caution Dear FreeSurfer experts: I am trying to run tracula in 4 subjects of a public dataset. I have encountered one error. I leave the output of terminal below. I also attach the configuration file. I hope you can follow from there. Sincerely, Andrade.

[Freesurfer] fsfast no run directories

External Email - Use Caution Dear FreeSurfer experts:I have some issues with "preproc-sess" because I cannot seem to get the setup of the directory structure or files to connect different things(the T1 subjects with functional bold or rest files). I have this output.  root@an

[Freesurfer] ERROR: Must specify input table of gradient vectors

External Email - Use CautionDear Anastasia Yendiki:I have tried to run TRACULA on 3 subjects as specified in configuration file attached. But the terminal output is: sh-3.2# trac-all -prep -c dmrirc.IXIdomainname: Command not found.Too many ('s.INFO: SUBJECTS_DIR is /Volumes/FREESUR

Re: [Freesurfer] Error in glmfit-sim cache

MAC. But this I hope is only temporary because makes no sense that a software works partially. Sincerely, Andrade. ERROR: > thresh = 4,0 must be 1.3, 2.0, 3.0, 4.0 I don't know what this refers to On 10/18/19 4:45 PM, Renew Andrade wrote: > External Email - Use C

[Freesurfer] mri_cvs_register error while diffusion imaging processing

External Email - Use Caution Dear FreeSurfer experts: I am trying to run Spatial Normalization but I cannot get the morph file because I get this error. I don’t know what to do with these libraries. Do I need to copy them from where they are in freesurfer to somewhere else in the

Re: [Freesurfer] Learning dti processing tutorial

n scan. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Renew Andrade Sent: Friday, October 18, 2019 5:02:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Learning dti processing tutorial External Email - Use Caution I am using a database of NITRC repo

Re: [Freesurfer] Learning fsfast tutorial

dti_L1.nii.gz dti_L3.nii.gz dti_MO.nii.gz dti_V1.nii.gz dti_V3.nii.gz ➜ rest git:(master) ✗ Sincerely, Andrade. look in sess01/bold, you should see 001 and 002. Do you? On 10/22/2019 9:40 AM, Renew Andrade wrote: External Email - Use Caution Dear experts: I am trying to run preproc

[Freesurfer] Learning fsfast tutorial

External Email - Use Caution Dear experts: I am trying to run preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run But the outcome is ERROR: no run directories found. What could be wrong? If you need more information let me know! Sincerely,

Re: [Freesurfer] Learning dti processing tutorial

What is the input file that you are supplying? Often this happens when the input it a multi-echo MPRAGE. If so, you can run mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz then use mprage.mgz as the input to recon-all On 10/12/2019 4:48 PM, Renew Andrade wrote: > External Em

Re: [Freesurfer] Error in glmfit-sim cache

External Email - Use Caution I have tried all the values it pinpoints to but none seem to work. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Learning dti processing tutorial

External Email - Use Caution Dear freesurfer experts: I am trying to learn dti processing. For using Tracula it appears there is a need for running "recon-all -all -i -s” on every subject before starting to run Tracula. But there seems to be a problem. I have a Parkinson dwi imag

[Freesurfer] Error in glmfit-sim cache

External Email - Use Caution Dear FreeSurfer experts: I have an issue when running correction for multiple comparisons. I enter this (mri_glmfit-sim --glmdir lh.IXI.glmdir --cache 4 abs —cap 0.05 --2spaces) in the terminal and I only receive messages of this sort (ERROR: thresh

[Freesurfer] Libraries not found Freeview ubuntu 18

External Email - Use Caution Dear FreeSurfer experts: I have a problem with Freeview running I ubuntu. Some libraries missing. I read this thread “https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63255.html

[Freesurfer] Fwd: Error in Analyze: Couldn't open ... fwhm10.fsaverage.mgz

External Email - Use Caution Dear FreeSurfer experts: I am processing in qdec 3 subjects with the GUI and I have this terminal output. Error in Analyze: Couldn't open /Applications/freesurfer/subjects/IXI_22_Guys_T1/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file. lh-Avg-

[Freesurfer] Error in Analyze: Couldn't open ... fwhm10.fsaverage.mgz

External Email - Use Caution Dear FreeSurfer experts: I am processing in qdec 3 subjects with the GUI and I have this terminal output. Error in Analyze: Couldn't open /Applications/freesurfer/subjects/IXI_22_Guys_T1/surf/lh.thickness.fwhm10.fsaverage.mgz or .mgh file. lh-Avg-

[Freesurfer] How to visualise DTI

External Email - Use Caution Dear community! I would like to know how can I use Freeview or any tool of FreeSurfer to visualise preprocessed DTI files from a database. They are in a standard output like it appears in Tracula output page of FreeSurfer wiki. It shouldn’t be a prob

[Freesurfer] x y dimension mismatch dt_recon

External Email - Use Caution Dear community: I have an issue that I have seen in the past still don´t know how to fix. Bval shows rows of 16 values and bvecs 17 values in one row only the rest 2 show 16 as apparently should be. What can I do? Sincerely, Andrade. __

[Freesurfer] About FreeSurfer source code

External Email - Use Caution Dear community: I was curious about how the software is made and I decided to write an email to Dr. Bruce Fischl who answered all of the questions I asked, but he gave me the input to ask these questions also in FreeSurfer Community. I first asked the

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution Hello again: I have downloaded this raw data from a database that’s the reason I’m not sure it is T1w but I think what they call ntdi it is. So when I run recon-all from this ntdi.nifti file it gives me a Talairach error. I send you the output termi

[Freesurfer] ERROR: dimension mismatch between y and X.

External Email - Use Caution Hello Community! I have an issue while running dt_recon because as can be seen in the output terminal there is some error in matrix dimensions. Renes-MacBook-Air-2:~ andraderenew$ dt_recon --b /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_pr

[Freesurfer] ERROR: input(s) cannot have multiple frames!

External Email - Use Caution Hello community! I have an issue while running recon-all -all in a dpi file. What do you suggest as a solution? Thank you! Renes-MacBook-Air-2:~ andraderenew$ recon-all -all -i /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/imaging-

[Freesurfer] Freeview modalSession has been exited prematurely - check for a reentrant call to endModalSession:

External Email - Use Caution Hello: I attach here the command output of an error that I have while using Freeview. It doesn’t allows me to read any file. sh-3.2# freeview -v \ > good_output/mri/T1.mgz \ > good_output/mri/wm.mgz \ > good_output/mri/brainmask.mgz \ > good_output/

[Freesurfer] ERROR: Transform file should be eddy_correct/eddy log file or .mat file

External Email - Use Caution Hello: I have a problem when running trac-all preprocessing. I have X11 and FSL installed. Not Matlab I don’t know if I need it I think only for fMRI. Sincerely, Andrade. Renes-MacBook-Air-2:diffusion_tutorial andraderenew$ trac-all -prep -c $TUTOR

[Freesurfer] Eddy correct command not found

External Email - Use Caution Dear community: I have a problem with trac-all processing with the tutorial data. sh-3.2# trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesur

[Freesurfer] Yendiki Anastasia config file

Here is the configuration file. I think is the default by tutorial. dmrirc.tutorial Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in th

Re: [Freesurfer] To Yendiki, Anastasia on TRACULA (Yendiki, Anastasia)

What is the configuration file or where can I find it? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is a

[Freesurfer] To Yendiki, Anastasia on TRACULA

Dear Anastasia: All the output I get is the if Expression Syntax. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to

[Freesurfer] tracula flags

Hello everyone! I have this problem with TRACULA. When I go to the second part of the tutorial I can´t keep going. I acknowledge that during the first part I have switch from tcsh to bash depending on errors but I’m not sure if that is normal or a mistake. The error is for example: trac-all -pre

[Freesurfer] bert log file

Hello everyone!I write to you because I can't get the process done in freesurfer. I attach the log file. Thank you! Mon Jan 22 01:16:35 CET 2018 /home/andraderenew/Downloads/SUBJECTS_DIR/bert /home/andraderenew/Downloads/freesurfer/bin/recon-all -i /home/andraderenew/Downloads/SUBJECTS_DIR/sample-

[Freesurfer] corRead(): can't open file /home/andraderenew/COR-.info

> Begin forwarded message: > > From: Renew Andrade > Subject: corRead(): can't open file /home/andraderenew/COR-.info > Date: 18 January 2018 at 12:15:49 CET > To: freesurfer@nmr.mgh.harvard.edu > > Hello: > I run the command to open freeview -v…(the installati

[Freesurfer] corRead(): can't open file /home/andraderenew/COR-.info

Hello: I run the command to open freeview -v…(the installation guide example in Bert) and I get the error in I point out in the subject of this email. Thanks for the help in advance! Sincerely, Rene Andrade. ___ Freesurfer mailing list Freesurfer@nmr