t;
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.edu
Subject: [Freesurfer
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
: [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
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
.
the 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
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
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 following mr
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
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
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 developers,
I'm trying
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
of 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
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
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
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
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
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
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
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:
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
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.
External Email - Use Caution
Ok, now we know stem2fname is the problem. I can’t reproduce the error
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 and rh.pial.T1.
rh.pial - rh.pial.T1
lh.pial - lh.pial.T1
Do you have lh.pial.T1 an
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
ther 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
External Email
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.
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
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
...@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
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
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
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
...@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
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 here
To: 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
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
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
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
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 mikel.gar...@alu.uclm.es
wrote:External Email - Use
CautionHello,I am
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
External Email - Use Caution
you can also use the python equivalent so you're not trying to run mex
files
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
, 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
; 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
: 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. All goes as planned up to this point
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
/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 downloaded
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
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 Mathworks
ias 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"
>
>
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 and
amygd
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
To: 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
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
, 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 ${subid
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
individual time point
rd.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 all 3 time points for this participant (is
this what yo
...@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
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
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 in longitudinal process step 3
-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
External
-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. Originally, I
: 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" claimin
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 longitudinal proc
: 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 run the long. processing pipeline but I
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:
"
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
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
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_HOMEoutput will be path to where installed
source $FREESURFER_HOME/SetUpFreeSurfer.sh
-
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:
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
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
...@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
7.2.0
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Turco, Isabella
Sent: Tuesday, May 2, 2023 10:55 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error Sourcing Freesurfer
External Email - Use Caution
Hello,
When trying to source Freesurfer
Of Kumar, Avnish
Sent: Tuesday, May 2, 2023 11:13 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error Sourcing Freesurfer
External Email - Use Caution
Could you post the ouitput of these two commands:
pwd
ls /usr/local/freesurfer
Best,
Avnish
From
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error Sourcing Freesurfer
External Email - Use Caution
Hello,
When trying to source Freesurfer version 7.1.1 using the command below, I’m
getting the error “No such file or directory.”
source /usr/local/freesurfer/fs-stable711-env
External Email - Use Caution
Hello,
When trying to source Freesurfer version 7.1.1 using the command below, I'm
getting the error "No such file or directory."
source /usr/local/freesurfer/fs-stable711-env-autoselect
Any guidance on potential solutions would be much appreciated!
External Email - Use Caution
I noticed the "-" used for the i and all is longer than the one used for
the s. It's a subtle difference and a problem if you are copying text from
Windows to Linux. Just replace the long hyphen with the short one.
On Sat, Apr 15, 2023 at 7:02 PM
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
Date: Monday, April 17, 2023 at 10:36
To: Freesurfer support list
Subject: Re: [Freesurfer] ERROR: flag i unrecognized
External Email - Use Caution
In the error message, the ‘-‘ is missing from options ‘i’ and ‘all
...@nmr.mgh.harvard.edu
On Behalf Of Francisco Polito haro
Sent: Saturday, April 15, 2023 8:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR: flag i unrecognized
External Email - Use Caution
I'm trying to start a scan but I can't get it to start the recon process
External Email - Use Caution
I'm trying to start a scan but I can't get it to start the recon process there,
I get an error, I don't know what I'm doing wrong. with the test subject of
BERT that marks the tutorial if it does, but with my file it doesn't, I attach
the message
:34
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] Error: mri_ca_register with non-zero
status 143
External Email - Use Caution
Bruce replied too.
We got to the same conclusion.
Yujing
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bennet Fauber
Sent: 14 April 2023 00:12:15
To: Freesurfer support list
Subject: Re: [Freesurfer] [FreeSurfer] Error: mri_ca_register with non-zero
status 143
External Email - Use Caution
It may also be the same signal if the operating
eeded it's maximum runtime?
>
> -Paul
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> on behalf of Krystal Xiwing Yau
>
> Sent: Thursday, April 13, 2023 3:02 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] [FreeSurfer] Erro
: [Freesurfer] [FreeSurfer] Error: mri_ca_register with non-zero
status 143
External Email - Use Caution
Sorry Yujing, Just seeing your reply now.
-Paul
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Huang, Yujing
Sent: Thursday
y synthsr again:
fspython -m pip install numpy==1.20.3
Best,
Avnish
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of hmarz...@student.ubc.ca
Sent: Wednesday, March 29, 2023 6:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] error wit
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Hi developers,
I'm Using freesurfer-darwin-macOS-dev.pkg (the ) which is developed in march
2023. Also my system is Apple M1 max (MacOS Ventura 13.2.1).
When I run synthsr, I receive an error:
mri_synthsr --i /Users/Hyperfine/028 --o
On Behalf Of Annie Cooper
Sent: Friday, March 17, 2023 2:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error When Running Recon-all- "Segmentation Fault"
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Hi there,
I am currently trying to run recon-all using a supercomputer at my
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Hi there,
I am currently trying to run recon-all using a supercomputer at my
university and am running into more errors than usual.
When trying to run recon-all from my terminal, I ran into this error
message:
[asurite@agave1:~/Desktop/T1_IMAGE]$
probably something wrong with your stimulus schedule (paradigm). Can you
send the X.mat (or Xtmp.mat)?
On 2/28/2023 12:12 PM, Caspar M. Schwiedrzik wrote:
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Hi!
I am running into an issue with fast_selxavg3b.
I am attempting a first level PPI analysis.
The
'-careg' probably is not needed for autorecon3 if it is run separately after
autorecon2.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Huang, Yujing
Sent: Tuesday, March 7, 2023 10:53 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] ERROR: cannot find or read transforms
Hi,
Can you try adding '-careg' to your recon-all command line after
-autorecon2/-autorecon3?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fraser Aitken
Sent: Tuesday, March 7, 2023 10:45 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR: cannot
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Hi all
I have upgraded to 7.3.2 and i seem to be having issues running recon all after
unto recon1. Basically, auto recon completes but after I have checked the brain
masks and go to run auto recon 2 and 3 i get the following error
reading 1 input
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Hi!
I am running into an issue with fast_selxavg3b.
I am attempting a first level PPI analysis.
The command is
mkanalysis-sess -fsd bold -native -delay -2/2 -notask -TR 2 -polyfit 6
-analysis [xxx] -funcstem [xxx] -runlistfile mooneyppi.list -nuisreg
...@nmr.mgh.harvard.edu
on behalf of Zeng, Victor (BIDMC -
Keshavan - Psychiatry)
Sent: Friday, February 17, 2023 1:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] error with synthsr
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Hi developers,
Using freesurfer-linux-centos7_x86_64-dev-20230216
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Hi developers,
Using freesurfer-linux-centos7_x86_64-dev-20230216-9bc2be6, I receive an error
following mri_synthsr.
It says :
get_data() is deprecated in favor of get_fdata(), which has a more predictable
return type. To obtain get_data()
: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Lizanne Arnoldy
Sent: Sunday, February 12, 2023 6:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR
fsaverage
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Dear freesurfer Experts
,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Huang, Yujing
Sent: Wednesday, January 11, 2023 9:11 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] ERROR: Label BA1_exvivo does not exist in
SUBJECTS_DIR fsaverage
Hi Junhong,
I don't see the error in your attached recon
Of Yu Junhong (Dr)
Sent: Wednesday, January 11, 2023 4:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] ERROR: Label BA1_exvivo does not exist in SUBJECTS_DIR
fsaverage
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Hi there,
I've been trying run recon-all on this public dataset MailScanner
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I have resolved by eliminating the option -nowhiten
It looks like the anatomical analysis is out of sync with the functional
analysis. Is is possible that you ran the functional analysis, then edited the
subject, then tried to rerun the
...@nmr.mgh.harvard.edu
On Behalf Of Nazanin Mirzaei
Sent: Friday, December 16, 2022 7:42 AM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] error/cannot create directory freesurfer
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Hello
when i use recon-all i get this message:
mkdir: cannot create directory
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