Re: [Freesurfer] Error in loading wmparc2diff.mgz

;> >>> 2. mri_info >>> /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri/wmparc2diff.mgz >>> >>> >>> >>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu < >>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *R

Re: [Freesurfer] Error in loading wmparc2diff.mgz

*Sent:* Friday, January 31, 2025 8:19 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz *External Email - Use Caution * Dear Yujing, Thank you for your prompt reply. Yes, it exists. $ ls -l

Re: [Freesurfer] Error in loading wmparc2diff.mgz

gt; freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ramesh Babu >> *Sent:* Friday, January 31, 2025 8:19 AM >> *To:* Freesurfer support list >> *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz >> >> >> >> *External Email - Use Caut

Re: [Freesurfer] Error in loading wmparc2diff.mgz

surfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Ramesh Babu > *Sent:* Friday, January 31, 2025 8:19 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Error in loading wmparc2diff.mgz > > > > *External Email - Use Caution* > > Dear Yujing,

Re: [Freesurfer] Error in loading wmparc2diff.mgz

: Friday, January 31, 2025 8:19 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in loading wmparc2diff.mgz External Email - Use Caution Dear Yujing, Thank you for your prompt reply. Yes, it exists. $ ls -l /mnt/data_analysis/freesurfer_data/diffusion_recons/sub01/mri

Re: [Freesurfer] Error in loading wmparc2diff.mgz

: Freesurfer support list Subject: Re: [Freesurfer] Error in loading wmparc2diff.mgz External Email - Use Caution Sorry, I forgot to attach the files with the earlier message. Dear Expert, I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is

[Freesurfer] Error in loading wmparc2diff.mgz

External Email - Use Caution Dear Expert, I am finding an error in loading wmparc2diff.mgz in freeview. The error report from the terminal is; $ freeview -v lowb.nii.gz $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green $SUBJE

Re: [Freesurfer] Error in recon-all

I can't see anything wrong either. Does it happen repeatedly? Can you try running it without the -parallel flag? On 1/7/2025 1:42 PM, Aaron Tanenbaum wrote: External Email - Use Caution You are correct. Attached is the correct one On Tue, Jan 7, 2025 at 8:08 AM Douglas N. Greve w

Re: [Freesurfer] Error in recon-all

Are you sure this is the right recon-all.log file? At the end it says it finished without error On 1/6/2025 4:12 PM, Aaron Tanenbaum wrote: External Email - Use Caution Hell All, I am testing recon-all and found that it returned with an error. I am not sure where the error is. The r

Re: [Freesurfer] Error in longitudinal hippocampal fields

oy any copies in any form immediately. From: "Iglesias Gonzalez, Juan E." mailto:jiglesiasgonza...@mgh.harvard.edu>> Subject: Re: [Freesurfer] Error in longitudinal hippocampal fields processing To: Freesurfer support list mailto:freesurfer@nmr.mgh.har

Re: [Freesurfer] Error in longitudinal hippocampal fields processing

@nmr.mgh.harvard.edu Subject: [Freesurfer] Error in longitudinal hippocampal fields processing 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

Re: [Freesurfer] Error During T2/FLAIR Pial Surface Refinement

attie F. Coor Hall Date: Wed, 9 Oct 2024 17:42:22 + From: "Fischl, Bruce R.,PHD" mailto:bfis...@mgh.harvard.edu>> Subject: Re: [Freesurfer] Error During T2/FLAIR Pial Surface Refinement To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: mailto

Re: [Freesurfer] Error During T2/FLAIR Pial Surface Refinement

guage Neuroscience) 975 S Myrtle Ave, Tempe, AZ 85281 | Lattie F. Coor Hall Date: Wed, 9 Oct 2024 17:42:22 + From: "Fischl, Bruce R.,PHD" Subject: Re: [Freesurfer] Error During T2/FLAIR Pial Surface Refinement To: Freesurfer support list Message-ID: < dm5pr04mb126171d02f1f51dffe6

Re: [Freesurfer] Error while opening Freeview on Linux

External Email - Use Caution Try downloading and installing the freesurfer .deb or.rpm linux package installer that matches your OS .. from,https://secure-web.cisco.com/1Me3-1hl0gfMcAF2vBsI1JUBKuzDpNWmT5AWDIQZn1zDSkYQTkZJwbxEHESlerG_wKis3UAnXfWQTsD0LLhgQmhZODSmg3KnPEdGIsZwKujygp6

[Freesurfer] Error while opening Freeview on Linux

External Email - Use Caution Dear Freesurfer team, I have Freesurfer installed on Linux. All Freesurfer commands work well, however, I am not able to open freeview. I get this error: _freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object

Re: [Freesurfer] Error During T2/FLAIR Pial Surface Refinement

Subject: [Freesurfer] Error During T2/FLAIR Pial Surface Refinement External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to refine pial surfaces with T2/FLAIR images as described here (MailScanner has detected a possible fraud attempt from "secure-web

[Freesurfer] Error During T2/FLAIR Pial Surface Refinement

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to refine pial surfaces with T2/FLAIR images as described here ( https://secure-web.cisco.com/1AH1BRBqXr5DfxhMfqvYMi7G1gSsW58-k5PUb3k7qBej25TzL4oJZblrUDWJjsLLjcoAP23YnnERxvXNWVp31VdS7Wz1q7Z9IGsbTfDYOtXS_IS2-N

Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer

rouble running those commands, but this is the lab computer "About Mac". Best,Ian JFrom: fsbuild <fsbu...@contbay.com> Sent: Monday, October 7, 2024 6:22 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] error: Bad CPU type in exe

Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer

Sequoia 15.0.1.From: fsbuild <fsbu...@contbay.com> Sent: Monday, October 7, 2024 4:36 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer  Please let us know the operating system name and revision

Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer

External Email - Use Caution I am running Sequoia 15.0.1. From: fsbuild Sent: Monday, October 7, 2024 4:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer Please let us know the

Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer

External Email - Use Caution  Please let us know the operating system name and revision running on the machine. - R. On Oct 7, 2024, at 16:13, Johnson, Ian wrote:External Email - Use CautionHello Free Surfer Pros, I am trying to run WMH-

[Freesurfer] error: Bad CPU type in executable WMH FreeSurfer

External Email - Use Caution Hello Free Surfer Pros, I am trying to run WMH-Synth-Seg on a different machine (2.4GHz Quad-Core Intel Core i5, Intel Iris Plus Graphics 655 1536 MB). I am getting the error message: "line 30: /Applications/freesurfer/dev/python/bin/python3: Bad CP

Re: [Freesurfer] Error in dt_recon

External Email - Use Caution Dear Douglas, Thank you so much. It's done. Regards Ramesh On Tue, Sep 17, 2024, 7:34 PM Douglas N. Greve wrote: > The argument to the --s flag should be the name of the subject as was > specified when you ran recon-all, eg > recon-all -i t1_SPGR.nii

Re: [Freesurfer] Error in dt_recon

The argument to the --s flag should be the name of the subject as was specified when you ran recon-all, eg recon-all -i t1_SPGR.nii  -s subjectname -all Then use dt_rcon -s subjectname ... On 9/12/2024 7:45 AM, Ramesh Babu wrote: External Email - Use Caution Dear All, I am new to dti

[Freesurfer] Error in dt_recon

External Email - Use Caution Dear All, I am new to dti analysis. I am trying analysis in a single subject. I set the environment as mentioned below. export DTI_DATA=export DTI_DATA=/mnt/data_analysis/mchp_projects/sneha/dti_analysis/FS_DTI_analysis export SUBJECTS_DIR=$DTI_DATA/su

Re: [Freesurfer] Error in SegmentSubfieldsT1Longitudinal (line 2148)

@nmr.mgh.harvard.edu Subject: [Freesurfer] Error in SegmentSubfieldsT1Longitudinal (line 2148) External Email - Use Caution Hello, I'm running the longitudinal hippocampal subfields module in ~300 individuals - it ran fine in most but with 8 i'm running into an error with the right

Re: [Freesurfer] Error saying cannot find my file for recon-all

It can't find the file struct.nii. You have to give it the full path to the file. It looks like $Users is not set to anything (blank) On 6/28/2024 12:03 AM, Lydia Luck wrote: External Email - Use Caution Hello- I am trying to do recon-all on my brain MRI and I’ve rewritten it so man

[Freesurfer] Error saying cannot find my file for recon-all

External Email - Use Caution Hello- I am trying to do recon-all on my brain MRI and I’ve rewritten it so many times I have absolutely no clue what is going wrong. Ultimately, the main error message I’m getting is that my file is not found. I’ve tried typing out the complete pat

Re: [Freesurfer] error using mri_em_register

***\n " You can't run recon-all '-autorecon2 -autorecon3' until you have successfully run autorecon1. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Michal Zamberg-Elad Sent: Wednesday, May 15, 2024 7:31 AM To: freesurfer@nmr.mgh.harvard

[Freesurfer] error using mri_em_register

External Email - Use Caution It does not create the nu.mgz file. Error logs are attached. The result is that when running recon all it cannot find the LH and RH files and then collapses. Darwin Kernel Version 21.3.0 iMac-Pro 21.3.0 Root: xnu-8019.80.24~20/RELEASE_X86_64 x86_64

Re: [Freesurfer] ERROR: cannot find AntsN4BiasFieldCorrectionFs in path

: [Freesurfer] ERROR: cannot find AntsN4BiasFieldCorrectionFs in path External Email - Use Caution Hi, I have installed FreeSurfer (freesurfer-linux-centos7_x86_64-7.4.1) into my research group's directory on the University cluster, using the tar archive. I source it with GROUPDIR= e

[Freesurfer] ERROR: cannot find AntsN4BiasFieldCorrectionFs in path

External Email - Use Caution Hi, I have installed FreeSurfer (freesurfer-linux-centos7_x86_64-7.4.1) into my research group's directory on the University cluster, using the tar archive. I source it with GROUPDIR= export FREESURFER_HOME=$GROUPDIR/software/freesurfer . $FREESURFE

Re: [Freesurfer] Error: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage!

help. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Pamela González Méndez Sent: Wednesday, April 24, 2024 9:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage! External Email

[Freesurfer] Error: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage!

External Email - Use Caution Hi everyone, While running a FreeSurfer command, I encountered the following error message: "Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage!" This error seems to indicate that the specified label is missing in the fsaverage directory wi

Re: [Freesurfer] Error using mris_transform in Freesurfer 7.4.1

Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Noemí Hostalet Sent: Tuesday, April 16, 2024 7:13 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error using mris_transform in Freesurfer 7.4.1 External Email - Use Caution Hi, I'm trying to run the followi

[Freesurfer] Error using mris_transform in Freesurfer 7.4.1

External Email - Use Caution Hi, I'm trying to run the following mris_transform command in Freesurfer version 7.4.1: mris_transform group1/z/Freesurfer/surf/lh.smoothwm group1/z/Freesurfer/mri/transforms/talairach.xfm group1/z/Freesurfer/surf/tal/lh.smoothwm.tal.asc But it's giv

[Freesurfer] ERROR: awk -f in Talairach registration and multibyte conversion failure; possibly due to region settings?

External Email - Use Caution Dear Freesurfer Developers, I installed Freesurfer 6.0.0 fresh on a Macbook Pro (2021) with M1 chip running macOS Monterey 12.5. I tried to run recon-all on both on the bert data shipped with freesurfer and my own brain data in .nii.gz format (sta

Re: [Freesurfer] ERROR: mri_ca_register with non-zero status 9

Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Lucas Alexis Ronat Sent: Tuesday, February 6, 2024 12:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] ERROR: mri_ca_register with non-zero status 9 External Email - Use Caution Hello FreeSurfer develope

[Freesurfer] ERROR: mri_ca_register with non-zero status 9

External Email - Use Caution Hello FreeSurfer developers, I'm trying to process structural MRI (T1w.nii) using the recon-all command but I get the following error: ERROR: mri_ca_register with non-zero status 9 Similar errors have been reported but I am unable to resolve this pro

Re: [Freesurfer] Error in mri_seg_overlap

Sorby-Adams, Annabel Date: Saturday, January 27, 2024 at 2:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error in mri_seg_overlap Hi Freesurfers, I am trying to compute DICE scores between 2 WMH-SynthSeg masks from a low-field image and high-field counterpart. I have co

[Freesurfer] Error in mri_seg_overlap

Hi Freesurfers, I am trying to compute DICE scores between 2 WMH-SynthSeg masks from a low-field image and high-field counterpart. I have co-registered the original images and used mri_binarize to isolate the WMH segmentations from other brain structures. I then used reg_resample to transform t

Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]FreeSurfer Error

you like From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of ERNEST KISSI Sent: Tuesday, January 9, 2024 2:06 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]FreeSurfer Error External Email - Use Caution Dear Freesurfer Developers, I am

Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

External Email - Use CautionOh, Good to know! Thank you so so much! Milly M. C. On Nov 17, 2023, at 3:04 PM, Douglas N. Greve wrote: You can't put math or brackets in the contrast file. Just use .333 .333 .333 -.333 -.333 -.333 0 0 0 0 On 11/16/2023 1

Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

You can't put math or brackets in the contrast file. Just use .333 .333 .333 -.333 -.333 -.333 0 0 0 0 On 11/16/2023 10:50 AM, Ludmila Midrigan wrote: External Email - Use Caution Dear Douglas, thank you for the reply. I am attaching it here. I usually create it  (using BASH)  as such

Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

External Email - Use Caution Dear Douglas, thank you for the reply. I am attaching it here. I usually create it (using BASH) as such: << echo “1 -1” > File_Name.mtxand have never had issues, however I have not used "[ ] " on my contrasts before... Thank you so so much for yo

Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

Can you send /data/Ghana_MRI_Data_lmid/StructT1/subjDir_FS_GHANA/Contrasts/GM_FM_ONE_minus_ZERO.mtx ? How did you create this file? A lot of word processors will add special characters that can cause a read failure. On 11/9/2023 12:33 PM, Ludmila Midrigan wrote: External Email - Use

Re: [Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

Can you send the command line, all the terminal output, and your fsgd file? On 11/3/2023 11:51 AM, Ludmila Midrigan wrote: External Email - Use Caution Hi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error: "error:

[Freesurfer] "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"

External Email - Use Caution Hi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error: "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast" I am only interested in a difference for G

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

: Freesurfer support list Cc: Maffei, Chiara, PHD ; Yendiki, Anastasia Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution Ok, now we know stem2fname is the problem. I can’t reproduce the error

Re: [Freesurfer] ERROR: could not configure recon-all parameters

n...@mgh.harvard.edu> To: "Freesurfer support list"<freesurfer@nmr.mgh.harvard.edu>; Cc: Sent: 2023. 10. 13. (금) 20:54 (GMT+09:00) Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters   lh.pial and rh.pial are created as symbol links to lh.pial.T1 a

Re: [Freesurfer] ERROR: could not configure recon-all parameters

From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of ??? Sent: Thursday, October 12, 2023 9:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters External Email - Use Caution Thank you for your swift reply. I will try that soon. I have

Re: [Freesurfer] ERROR: could not configure recon-all parameters

s this another recon-all error or is this just my data problem? Thank you in advance. Best, Alice -Original Message- From: "fsbuild" To: ; Cc: ; Sent: 2023. 10. 13. (금) 10:04 (GMT+09:00) Subject: Re: [Freesurfer] ERROR: could not configure recon-all parameters Exte

Re: [Freesurfer] ERROR: could not configure recon-all parameters

External Email - Use Caution  It looks like permissions on the installed freesurfer files and/or what you set FREESURFER_HOME to may not be correct. I would delete your current freesurfer install and then use the Mac installer package (.pkg) file to install the 7.4.1 release.  Th

Re: [Freesurfer] ERROR: could not configure recon-all parameters

External Email - Use Caution Hi, On top of the email I sent earlier, I also get the next error line that says: ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary fi

[Freesurfer] ERROR: could not configure recon-all parameters

External Email - Use Caution Good day, I get the following error message when I run recon-all: ERROR: could not configure recon-all parameters /Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file I went thro

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

...@nmr.mgh.harvard.edu On Behalf Of Lawless, Dylan Sent: Wednesday, October 11, 2023 10:39 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution I ran this

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

oun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: Wednesday, October 11, 2023 9:32 AM To: Freesurfer support list Cc: Maffei, Chiara, PHD ; Yendiki, Anastasia Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. Exter

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

ylan Sent: Wednesday, October 11, 2023 10:01 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution Could you point me towards the correct log file? I am unable to loca

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

Sent: Tuesday, October 10, 2023 10:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution There should be a log for the command you ran. I’m wondering

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

...@nmr.mgh.harvard.edu On Behalf Of Lawless, Dylan Sent: Tuesday, October 10, 2023 10:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution Sure thing, I have attached the

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

on behalf of Huang, Yujing Sent: Tuesday, October 10, 2023 9:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution The error that you cut and paste

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution Hello, I am attempting to create a freesurfer v7.2.0 docker container that can run tracula on the freesurfer outputs

[Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

External Email - Use Caution Hello, I am attempting to create a freesurfer v7.2.0 docker container that can run tracula on the freesurfer outputs, however, I am unable to get past the intra-subject registration step without receiving the following error:   --s sub-01 --mov

Re: [Freesurfer] Error mri_ca_register

Subject: [Freesurfer] Error mri_ca_register External Email - Use Caution Hello, I am having a problem running Freesurfer on Linux server Centos 7. I installed freesurfer correctly and when I try to run the command: recon -all -s sample -I sample-001.mgz -all I get an error message

[Freesurfer] Error mri_ca_register

External Email - Use Caution Hello, I am having a problem running Freesurfer on Linux server Centos 7. I installed freesurfer correctly and when I try to run the command: recon -all -s sample -I sample-001.mgz -all I get an error message : mri_ca_register with non-zero status 9

Re: [Freesurfer] error in my software

External Email - Use Caution  Hello Mikel, Can you send us more details like terminal output or perhaps screenshot from the terminal that shows the error ? - R. On Aug 4, 2023, at 15:54, MIKEL GARCÍA AGUIRRE wrote:External Email - Use Caution 

[Freesurfer] error in my software

External Email - Use Caution Hello, I am working with a MacBook M1 from 2020 and I downloaded two versions of Freesurfer. The first one was the 7.4.1 version, but I have also tried the 7.2.0 version. The problem that I have is that whenever I tried to upload one file, the progr

Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline

External Email - Use Caution you can also use the python equivalent so you're not trying to run mex files https://secure-web.cisco.com/1g8E_AOm3VXmhvpy6veMl40Kme1LNWWT1lb_WgkRyBt5Etmh-v8ma6TKJSQWDj5TH-KVfoGp0346fsQdTj15hy3nF8ALVxGteNWCIMe8wGmljgqEaDxSxez7d2aqs5WYVsvWzMc3YIBWkKtNAU

Re: [Freesurfer] Error Help

gt; On Behalf Of Misque Boswell > Sent: Monday, July 3, 2023 12:30 PM > To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Error Help > > External Email - Use Caution > > Thank you, Yujing. Here it

Re: [Freesurfer] Error Help

, 2023 12:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] Error Help External Email - Use Caution Thank you, Yujing. Here it is: Misques-MBP-3 / % /Applications/freesurfer/7.4.1/bin/lta_convert -all-info 7.4.1 ProgramName: lta_convert ProgramArguments: /Applications/freesurfer

Re: [Freesurfer] Error Help

; Yujing > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Misque Boswell > Sent: Monday, July 3, 2023 11:44 AM > To: Freesurfer support list <m

Re: [Freesurfer] Error Help

On Behalf Of Misque Boswell Sent: Monday, July 3, 2023 11:44 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error Help External Email - Use Caution Hello Yujing, Thank you for your response. I followed the directions for setup and sourced SetUpFreeSurfer.sh as you stated. A

Re: [Freesurfer] Error Help

External Email - Use Caution Hello Yujing, Thank you for your response. I followed the directions for setup and sourced SetUpFreeSurfer.sh as you stated. All goes as planned up to this point. Misques-MBP-3 / % export FREESURFER_HOME=Applications/freesurfer/7.4.1 Misques-MBP-3

Re: [Freesurfer] Error Help

l 2. ls -l /lta_convert Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Misque Boswell Sent: Sunday, July 2, 2023 8:40 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error Help External Email - Use Caution Hi, I am new to FS and recently down

[Freesurfer] Error Help

External Email - Use CautionHi, I am new to FS and recently downloaded the package per instructions on your site. I set up the path and everything seems to be fine until I attempt to use any functions.I have searched for answers on this error, but I cannot seem to find anything so I

Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline

External Email - Use Caution The  .mexa64 file is a matlab shared library and that error is from the linker saying it is not allowed to link in that library.  Note that it did not say there was a permission denied error or that the .mexa64 file could not be found.   This Mathwo

Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline

Iglesias Gonzalez, Juan E." > Subject: Re: [Freesurfer] Error running hippocampus subfields and > amygdala nuclei segmentation pipeline > To: Freesurfer support list > Message-ID: > > > > Content-Type: text/plain; charset="windows-1252" > &

Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline

n managing the list at freesurfer-ow...@nmr.mgh.harvard.edu -- Message: 8 Date: Tue, 13 Jun 2023 16:07:34 + From: "Iglesias Gonzalez, Juan E." Subject: Re: [Freesurfer] Error running hippocampus subfields

Re: [Freesurfer] Error with running retinotopy glm

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Loïc Daumail Date: Monday, June 5, 2023 at 5:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] Error with running retinotopy glm External Email - Use Caution Dear Freesurfer experts, To follow up on my previous email

Re: [Freesurfer] Error: MRInormFindControlPoints: could not find enough control points

: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error: MRInormFindControlPoints: could not find enough control points External Email - Use Caution Dear Freesurfer experts, I was trying this command: $ recon-all -s Desikan -i /path/to/nii -all, to generate the anno files. But it

[Freesurfer] Error: MRInormFindControlPoints: could not find enough control points

External Email - Use CautionDear Freesurfer experts,I was trying this command: $ recon-all -s Desikan -i /path/to/nii -all, to generate the anno files.But it ends up with the errors of MRInormFindControlPoints: could not find enough control points The .nii file I am using is the vol

Re: [Freesurfer] Error in longitudinal process step 3

Huang, Yujing Sent: Tuesday, June 13, 2023 12:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] Error in longitudinal process step 3 External Email - Use Caution In your script, this line selects all 4 directories (6008, 6008_tp1, 6008_tp2, 6008_tp3) timepoints=`ls -d1 ${

Re: [Freesurfer] Error in longitudinal process step 3

mgh.harvard.edu On Behalf Of Taylor, Lisa Sent: Tuesday, June 13, 2023 2:58 PM To: Freesurfer support list Subject: Re: [Freesurfer] Error in longitudinal process step 3 External Email - Use Caution Hi Yujing, The recon-all.logs I sent previously were the recon-all was done for each i

Re: [Freesurfer] Error in longitudinal process step 3

t, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Taylor, Lisa Sent: Tuesday, June 13, 2023 12:55 PM To: Freesurfer support list Subject: Re: [Freesurfer] Error in longitudinal process step 3 External Email - Use Caution Hi Yujing, I have attached recon-all.log for a

Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline

...@nmr.mgh.harvard.edu on behalf of Mengjie Huang Date: Tuesday, June 13, 2023 at 8:12 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline External Email - Use Caution Hello FreeSurfer developers, I am

[Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline

External Email - Use Caution Hello FreeSurfer developers, I am writing to seek help regarding an issue I encountered when trying to run the hippocampus subfields and amygdala nuclei segmentation pipeline (please see the error message attached below). I am running FreeSurfer V.7.

Re: [Freesurfer] Error in longitudinal process step 3

time points for recon-all base processing? Attached is the long processing. Can you attach recon.log for base processing? Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Taylor, Lisa Sent: Monday, June 12, 2023 4:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] Error

Re: [Freesurfer] Error in longitudinal process step 3

6008] $cat base-tps 6008_6008 6008_tp1 6008_tp2 6008_tp3 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: Monday, June 12, 2023 1:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Error in longitudinal process step 3

Re: [Freesurfer] Error in longitudinal process step 3

freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Taylor, Lisa Sent: Monday, June 12, 2023 3:18 PM To: Freesurfer support list Subject: Re: [Freesurfer] Error in longitudinal process step 3 External Email - Use Caution Hi Yujing, Yes, that is correct that 6008_tp1 is timepoint 1. Ori

Re: [Freesurfer] Error in longitudinal process step 3

t Subject: Re: [Freesurfer] Error in longitudinal process step 3 External Email - Use Caution Hi Lisa, I’m wondering what your naming convention is. Here is tutorial page for longitudinal processing: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com&quo

Re: [Freesurfer] Error in longitudinal process step 3

.edu On Behalf Of Huang, Yujing Sent: Monday, June 12, 2023 9:59 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in longitudinal process step 3 External Email - Use Caution Hi Lisa, I'm wondering what your naming convention is. Here is tutorial page for lo

Re: [Freesurfer] Error in longitudinal process step 3

on-all commands? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Taylor, Lisa Sent: Thursday, June 8, 2023 5:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error in longitudinal process step 3 External Email - Use Caution Hi, I am trying to

Re: [Freesurfer] Error with running retinotopy glm

External Email - Use Caution Dear Freesurfer experts, To follow up on my previous email, I also tried the same code on a different PC with Ubuntu 22.02.4 LTS and FreeSurfer version 7.4 This time, I also get an error at the stage of running selxavg3-sess: " /home/tonglab/Document

[Freesurfer] Error with running retinotopy glm

External Email - Use Caution Dear FreeSurfer experts, I am trying to perform a retinotopy analysis using fs-fast with Freesurfer version 7.3.2 on a Mac OS Monterey Version 12.6.2 Here is the error I am having (I saw this same error in the archive, but I wasn't able to find any so

Re: [Freesurfer] source freesurfer error

22:27 Para: freesurfer@nmr.mgh.harvard.edu Cc: phbarra...@hotmail.com Assunto: Re: [Freesurfer] source freesurfer error Try using $ instead of # to tell the linux shell to expand an environment variable, e.g., here to the path of where freesurfer was installed. echo $FREESURFER_HOME

Re: [Freesurfer] source freesurfer error

External Email - Use Caution Try using $ instead of # to tell the linux shell to expand an environment variable, e.g., here to the path of where freesurfer was installed.   echo $FREESURFER_HOME

  source $FREESURFER_HOME/SetUpFreeSurfer.sh

[Freesurfer] source freesurfer error

External Email - Use Caution Hi everyone! I am trying to run freesurfer on a windows machine using ubuntu but I am having trouble with the source command When I try to source freesurfer i get the following message: source #FREESURFERHOME/SetUpFreeSurfer.sh -bash: source: filena

Re: [Freesurfer] error with mri_convert from nii made from TIFFs

External Email - Use Caution Hi Andrew, Freesurfer currently doesn’t support RGB and RGBA datatypes. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Andrew M Sent: Sunday, May 7, 2023 3:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer

[Freesurfer] error with mri_convert from nii made from TIFFs

External Email - Use Caution I have a head CT comprised of 186 .tiff files from the original study. I converted these files to .nii by using MRIcroGL's TIFF->DICOM converter, and now tried using mri_convert -rl to get it into fs space. However, I get the errors: error: No such fil

Re: [Freesurfer] Error Sourcing Freesurfer

...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: Tuesday, May 2, 2023 11:24 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error Sourcing Freesurfer External Email - Use Caution Hi Isabella, ‘fs-stable711-env-autoselect’ should be the string passed to fsenv script. For

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