[Freesurfer] TRACULA error: lowb_brain_mask.bbr.nii.gz

External Email - Use Caution Hi FreeSurfers, I am attempting to run tracula on longitudinal DTI data however during trac-all -prep the process fails because it does not generate lowb_brain_mask.bbr.nii.gz from mri_concat. #-

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz External Email - Use Caution Hi Lauren. Would you send me the trac-preproc ( /your path to/freesurfer/bin ) file, you corrected? best regards Woo-Suk, Tae On Tue, Oct 31, 2023

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

harvard.edu> on behalf of Woo-Suk Tae < > woos...@gmail.com> > *Sent:* Saturday, October 28, 2023 10:34 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] TRACULA Error: Subregion Segmentation > aparc+aseg+thalnuc.nii.gz > > > External Email -

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

: (650)-725-1716 From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Woo-Suk Tae Sent: Saturday, October 28, 2023 10:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

External Email - Use Caution Hi, Lauren Stephens. If you change some codes in trac-preproc ( in path/freesurfer/bin ), you can get an aparc+aseg+thalnuc.nii.gz file without error, and make subthalamic nuclei related tracks. #chage codes from set cmd = mri_binarize set cmd =

Re: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz

@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA Error: Subregion Segmentation aparc+aseg+thalnuc.nii.gz External Email - Use Caution Hi FreeSurfers, I am trying to troubleshoot an error during TRACULA preprocessing and the issue seems related to the creation of aparc+aseg+thalnuc.nii.gz

[Freesurfer] Freesurfer TRACULA Error

External Email - Use Caution Hello FreeSurfer Developers, I am trying to apply TRACULA for the reconstruction of white matter pathways but I am getting an error when running the trac-all command which I haven’t managed to resolve. The TRACULA is applied on an MRI sample from

Re: [Freesurfer] Tracula error in path construction

of output. Please attach your entire trac-all.log file. Thanks, Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Shanika Jayakody Sent: Monday, July 25, 2022 3:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error in path

Re: [Freesurfer] Tracula error in path construction

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia Sent: Thursday, July 21, 2022 4:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error in path construction Could be that you reached a memory limit? If the same

Re: [Freesurfer] Tracula error in path construction

To: Freesurfer support list Subject: [Freesurfer] Tracula error in path construction External Email - Use Caution Dear Anastasia I am running tracula on FreeSurfer 7.2. It worked fine on a linux computer now I am changing to a Cloud workstation. Attached is my Configuration file

[Freesurfer] Tracula error in path construction

External Email - Use Caution Dear Anastasia I am running tracula on FreeSurfer 7.2. It worked fine on a linux computer now I am changing to a Cloud workstation. Attached is my Configuration file. For this person the pipeline worked without errors until path reconstruction but

Re: [Freesurfer] Tracula error

support list Subject: Re: [Freesurfer] Tracula error Hello, I wanted to follow up on this question. I appreciate it much if you could suggest me any solutions. I checked my space and I have 3.5 T free space, so It’s definitely not a space problem. Thanks, Mona On Dec 14, 2021, at 12:59 PM

Re: [Freesurfer] Tracula error

2:41 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Tracula error How much space would I need to run this? Thanks, Mona On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> w

Re: [Freesurfer] Tracula error

Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Tracula error How much space would I need to run this? Thanks, Mona On Dec 14, 2021, at 12:40 PM, Yendiki, Anastasia mailto:ayend...@mgh.harvard.edu>> wrote: Any chance you're low on disk space? _

Re: [Freesurfer] Tracula error

Is there a dmri/data.nii.gz? Can you run mri_info on it please? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Nasiriavanaki, Zahra,M.D. Sent: Tuesday, December 14, 2021 12:41 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error

Re: [Freesurfer] Tracula error

rfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Nasiriavanaki, Zahra,M.D. mailto:znasiriavan...@mgh.harvard.edu>> Sent: Tuesday, December 14, 2021 12:18 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [

Re: [Freesurfer] Tracula error

Any chance you're low on disk space? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Nasiriavanaki, Zahra,M.D. Sent: Tuesday, December 14, 2021 12:18 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error Yes. dmri.bedpostX has

Re: [Freesurfer] Tracula error

esday, December 14, 2021 11:40 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Tracula error Hello, I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know wha

Re: [Freesurfer] Tracula error

: [Freesurfer] Tracula error Hello, I was running the "trac-all -bedp” section, when I got the below error. I appreciate it much if you please let me know what the issue is. Thanks, Mona - Bedpostx Monitor - An error ocurred. Please check file /autofs/cluster/guptagp/zn025/ALD/subje

Re: [Freesurfer] Tracula error

asiriavanaki, Zahra,M.D. mailto:znasiriavan...@mgh.harvard.edu>> Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Tracula error Hi Anastasia, I did add the ANTs to my path, but am still getting that same error.

Re: [Freesurfer] Tracula error

...@nmr.mgh.harvard.edu on behalf of Nasiriavanaki, Zahra,M.D. Sent: Tuesday, December 7, 2021 1:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error Hi Anastasia, I did add the ANTs to my path, but am still getting that same error. I adde the path : setenv ANTSPATH /usr/pubsw/packages

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

.haen...@upd.unibe.chSent:Thursday, November 25, 2021 1:40 AMTo:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals fileExternal Email - Use CautionDear Anastasiacat $FSLDIR/etc/fslversion reported6.0.5.1:57b01774I guess its the n

Re: [Freesurfer] Tracula error

12:21 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Tracula error Hello, I’ve been running the trac-all -prep step and I faced this error: ConvertTransformFile 3 /autofs/cluster/gu

Re: [Freesurfer] Tracula error

Subject: [Freesurfer] Tracula error Hello, I’ve been running the trac-all -prep step and I faced this error: ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt

[Freesurfer] Tracula error

Hello, I’ve been running the trac-all -prep step and I faced this error: ConvertTransformFile 3 /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat /autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras ConvertTransformFile:

Re: [Freesurfer] TRACULA error

: Thursday, December 2, 2021 2:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA error External Email - Use Caution Hello Freesurfer Team, I am trying to get TRACULA running on two different machines (Macbook Pro OS 11.6 and Mac desktop OS 10.14.6). I get the same error

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of juergen.haen...@upd.unibe.ch Sent: Thursday, November 25, 2021 1:40 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file External Email - Use

[Freesurfer] TRACULA error

External Email - Use Caution Hello Freesurfer Team, I am trying to get TRACULA running on two different machines (Macbook Pro OS 11.6 and Mac desktop OS 10.14.6). I get the same error message on both devices, which is: domainname: Command not found. ERROR: for B0 distortion

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

t;mailto:juergen.haen...@upd.unibe.ch> mailto:juergen.haen...@upd.unibe.ch>> Sent: Wednesday, November 24, 2021 12:53 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] TRACULA error wrt to d

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file External Email - Use Caution Dear Anastasia when I type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied. this is the right path where fsl is installed. however, I can start FSL GUI and also other FSL

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

gt;> on behalf of juergen.haen...@upd.unibe.ch<mailto:juergen.haen...@upd.unibe.ch> mailto:juergen.haen...@upd.unibe.ch>> Sent: Tuesday, November 23, 2021 9:36 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> mailto:freesurfer@nmr.mgh.harvard.edu>> S

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

Hi Jürgen - What's your $FSLDIR set to? Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of juergen.haen...@upd.unibe.ch Sent: Tuesday, November 23, 2021 9:36 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA error wrt

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

reesurfer@nmr.mgh.harvard.edu> mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file External Email - Use Caution Dear Anastasia thank you for providing the bug fix. It works and solved our problem. However, another (old) problem

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

surfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file External Email - Use Caution Dear Anastasia thank you for providing the bug fix. It works and solved our problem. However, another (old) problem occurred wrt the field map for which we did not find any so

Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

on behalf of juergen.haen...@upd.unibe.ch Sent: Wednesday, October 27, 2021 8:19 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file External Email - Use Caution Dear TRACULA experts I try to run TRACULA FS7.2 on a Linux machine and get

[Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

External Email - Use Caution Dear TRACULA experts I try to run TRACULA FS7.2 on a Linux machine and get the following error (see below). A similar problem has already been reported in the archives, but I found no solution.

Re: [Freesurfer] TRACULA error: missing output volume name

support list Subject: Re: [Freesurfer] TRACULA error: missing output volume name Hi Shanika - Can you try separating the "=" signs from the variable names in the config file with a space? Best, Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] TRACULA error: missing output volume name

Freesurfer support list Subject: Re: [Freesurfer] TRACULA error: missing output volume name External Email - Use Caution External Email - Use Caution Hi Anastasia Thanks so much for your reply. I have attached herewith the scripts/log file -please let me know if you need any

Re: [Freesurfer] TRACULA error: missing output volume name

, Anastasia Sent: Wednesday, March 17, 2021 5:40 PM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA error: missing output volume name Hi Shanika - Can you please send the full log file from scripts/trac-all.log? It's hard to figure out what causes the error without seeing the full

Re: [Freesurfer] TRACULA error: missing output volume name

on behalf of Shanika Jayakody Sent: Wednesday, March 17, 2021 4:04 PM To: Freesurfer support list Subject: [Freesurfer] TRACULA error: missing output volume name External Email - Use Caution External Email - Use Caution Dear FreeSurfer team I have been running TRACULA

[Freesurfer] TRACULA error: missing output volume name

External Email - Use Caution Dear FreeSurfer team I have been running TRACULA for some time now but recently, I come across a message "missing output volume name" and I cannot do preprocessing in new or old subjects (even subjects who completed preprocessing without error) I

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

support list Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed} Hi Oshadi - That does not sound normal. Is there anything wrong with the FreeSurfer segmentation of this subject? Anastasia. From: Shanika Jayakody Sent

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed} External Email - Use Caution Hi Anastasia Thanks so much- I think I got the error due to the format of the bvecs and bvals Trac-all is running but for one person it is running for almost 5 days now- I assume that can't

Re: [Freesurfer] Tracula error

To: Freesurfer support list Subject: [Freesurfer] Tracula error External Email - Use Caution Hello all, I am trying to run Tracula for one of my subjects and after creating the configuration file I run trac-all -prep -c /path/to/config/file but I am getting this error: FSLDIR: Undefined variable. I

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed} The two formats that you sent are not equivalent. In the version where the gradient vectors saved in columns, the first 2 columns are: 0 -0.793264 0 -0.394167 0 0.464074 In the version

[Freesurfer] Tracula error

External Email - Use Caution Hello all, I am trying to run Tracula for one of my subjects and after creating the configuration file I run trac-all -prep -c /path/to/config/file but I am getting this error: FSLDIR: Undefined variable. I have run the SetUpFreeSurfer.sh script and

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed} CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

but get the same error Thank you very much, Oshadi From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Shanika Jayakody Sent: Tuesday, October 27, 2020 2:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error: run list is longer than subject

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

hat causes this. If you have any suggestion please let me know Thanks, Oshadi From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia Sent: Tuesday, October 27, 2020 2:39 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error

Re: [Freesurfer] Tracula error: run list is longer than subject list

_ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Shanika Jayakody Sent: Monday, October 26, 2020 8:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list External Email - Use Caution I am double checking so the command i

Re: [Freesurfer] Tracula error: run list is longer than subject list

: Monday, October 26, 2020 5:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error: run list is longer than subject list What goes after "-c" in the trac-all command should be the configuration file, not the nifti file. From: Shanik

Re: [Freesurfer] Tracula error: run list is longer than subject list

hing-looking forward to hear from you. Many thanks, Oshadi From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia Sent: Monday, October 26, 2020 11:05 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error: run list is longer t

Re: [Freesurfer] Tracula error: run list is longer than subject list

something-looking forward to hear from you. Many thanks, Oshadi From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia Sent: Monday, October 26, 2020 11:05 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula error: run list

Re: [Freesurfer] Tracula error: run list is longer than subject list

External Email - Use Caution From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yendiki, Anastasia Sent: Monday, October 19, 2020 8:33 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error: run list is longer

Re: [Freesurfer] Tracula error: run list is longer than subject list

: [Freesurfer] Tracula error: run list is longer than subject list Make sure to use "subjlist", not "sublist". If that is not the issue, then please attach your log file and configuration file - it's hard to guess the issue without more information. Best, Anastasia. _

Re: [Freesurfer] Tracula error: run list is longer than subject list

vard.edu on behalf of Shanika Jayakody Sent: Monday, October 19, 2020 2:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error: run list is longer than subject list External Email - Use Caution Hello, I have been trying to run trac-all on a DWI of a participant,

[Freesurfer] Tracula error: run list is longer than subject list

External Email - Use Caution Hello, I have been trying to run trac-all on a DWI of a participant, but I keep getting the error "run list is longer than subject list" I have created a configuration file setting sublist and runlist to just one subject so I am not sure what the

Re: [Freesurfer] Tracula error

: [Freesurfer] Tracula error Hi Yasemin - It looks like the unix shell doesn't like that there are spaces after the "\" in a few lines: 1723_base \ 1741_base \ 1725-2/eddy_with_repol.nii.gz \ Best, Anastasia. From: freesurfer-boun...@nmr.mgh.h

Re: [Freesurfer] Tracula error

u, Yasemin Sent: Tuesday, September 29, 2020 11:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error Hi, I am trying to run trac-all using a configuration file for 30 subjects with longitudinal data, and keep getting the following errors: Too many ('s. ERROR: must speci

[Freesurfer] Tracula error

Hi, I am trying to run trac-all using a configuration file for 30 subjects with longitudinal data, and keep getting the following errors: Too many ('s. ERROR: must specify as many DWI dicoms as subjects I looked through my file line by line and looked at similar posts on the archives but could

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

To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors Hi, I have been trying different ways to troubleshooting this error without success. I am pasting here the whole error when I try to run "trac-all -prep -c" in the D

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

Hi, I have been trying different ways to troubleshooting this error without success. I am pasting here the whole error when I try to run "trac-all -prep -c" in the Dev version: INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon INFO: Diffusion root is

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

Hello Dear Freesurfer Developers, I am attempting to run Tracula in the last to subject of my study (I had processed all the other subjects using the same script without problems). However, when I try to run the scrip bellow, I am having the error: " ERROR: Must specify input table of gradient

[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

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

ber 21, 2019 9:11 AM To: Freesurfer Support List Subject: [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

[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.

Re: [Freesurfer] TRACULA error - MRISread could not open file

: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Daniel Callow Sent: Thursday, October 10, 2019 9:20 AM To: Freesurfer support list Subject: Re: [Freesurfer] TRACULA error - MRISread could not open file External Email - Use Caution Hello, It isn't an error with recon-all

Re: [Freesurfer] TRACULA error - MRISread could not open file

tober 10, 2019 9:01:25 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] TRACULA error - MRISread could not open file > > > External Email - Use Caution > > Hello, > > I am running tracula on some of my DTI data and have had no issues for > most of

Re: [Freesurfer] TRACULA error - MRISread could not open file

: Thursday, October 10, 2019 9:01:25 AM To: Freesurfer support list Subject: [Freesurfer] TRACULA error - MRISread could not open file External Email - Use Caution Hello, I am running tracula on some of my DTI data and have had no issues for most of my subjects. However, for one of

[Freesurfer] TRACULA error - MRISread could not open file

External Email - Use Caution Hello, I am running tracula on some of my DTI data and have had no issues for most of my subjects. However, for one of them I get the following error after mri_segreg MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not open

Re: [Freesurfer] Tracula error -path

@nmr.mgh.harvard.edu Subject: [Freesurfer] Tracula error -path External Email - Use Caution Hi list, Im using TRACULA in a dataset of 60 subjects. for 56 subjects everything is fine, but for 4 subjects I had the following error: >> ncpts: Subscript out of range. For these subjects TRACUL

[Freesurfer] Tracula error -path

External Email - Use Caution Hi list, Im using TRACULA in a dataset of 60 subjects. for 56 subjects everything is fine, but for 4 subjects I had the following error: >> ncpts: Subscript out of range. For these subjects TRACULA does not reconstruct the file

Re: [Freesurfer] [tracula] error running trac-all -prep

Hi all, sorry for reviving this super old thread, but it came up here as well with Freesurfer 6.0.0. > This is an Ubuntu-related error that has surfaced recently because in > Ubuntu /bin/sh is not a bash shell any more. To get around this, you can > edit the first line of the scripts

[Freesurfer] TRACULA error "R: Subscript out of range"

Hi all, I’m trying to run TRACULA on a single subject’s data, but trac-all -prep is exiting with the output below. Most notably, I think, is the section of the output that says "R: Subscript out of range.” repeatedly and then the section afterwards that says “keeping frames 0 1 2 3 4 5 6 7 8

Re: [Freesurfer] TRACULA - error

, 2017 4:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA - error Hi, I’m running tracula using the following command: (Note: I’m replacing actual paths with made up paths) trac-all -prep -c /path/to/my/config.sh And for some reason it stops running while working

[Freesurfer] TRACULA - error

Hi, I'm running tracula using the following command: (Note: I'm replacing actual paths with made up paths) trac-all -prep -c /path/to/my/config.sh And for some reason it stops running while working on the first subject (creates the folder for the first subject), with this error: if: Expression

Re: [Freesurfer] TRACULA ERROR!!

support list Subject: Re: [Freesurfer] TRACULA ERROR!! Dear Anastasia, I used dicom images to run my subjects, and yes, those freesurfer recons were found in SUBJECTS_DIR in my configuration file. Thanks. best, Ariel On Mon, Aug 7, 2017 at 2:39 PM, Yendiki, Anastasia <ayend...@mgh.harvard.

Re: [Freesurfer] TRACULA ERROR!!

gt; l...@union.edu> > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Date: Monday, August 7, 2017 at 12:00 AM > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] TRACULA ERROR!! > > Dear fellow res

Re: [Freesurfer] TRACULA ERROR!!

t;mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] TRACULA ERROR!! Dear fellow researchers, I am running tracula pre-processing step, and the computer showed an error message: Location of aparc+a

[Freesurfer] TRACULA ERROR!!

Dear fellow researchers, I am running tracula pre-processing step, and the computer showed an error message: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP

Re: [Freesurfer] tracula error message

@gmail.com>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, July 21, 2017 at 9:41 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>

[Freesurfer] tracula error message

Hi Freesurfers, Could you help me interpret this error message? I am attempting to run TRACULA using version 6 on a MacBook Pro OS X El Capitan Version 10.11.3 helpdesks-MacBook-Pro-2:R01_DTI crc$ trac-all -prep -c dmrirc.example1 INFO: SUBJECTS_DIR is /Users/crc/Documents/myprojects/R01_DTI

Re: [Freesurfer] TRACULA Error in virtualbox

on behalf of Alexander Zent > [az...@pdx.edu] > *Sent:* Wednesday, November 23, 2016 6:12 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] TRACULA Error in virtualbox > > I am trying to run TRACULA and keep getting the error FSLDIR: Undefined > Variable. I have

Re: [Freesurfer] TRACULA Error in virtualbox

...@pdx.edu] Sent: Wednesday, November 23, 2016 6:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TRACULA Error in virtualbox I am trying to run TRACULA and keep getting the error FSLDIR: Undefined Variable. I have looked at the answers to this question that have been previously posted

[Freesurfer] TRACULA Error in virtualbox

I am trying to run TRACULA and keep getting the error FSLDIR: Undefined Variable. I have looked at the answers to this question that have been previously posted but cannot seem to remedy this problem. I'm running freesurfer 5.3 via virtualbox on windows. I have applied for a license and added that

Re: [Freesurfer] Tracula Error -preproc Segmentation fault (core dumped)

Hi Kristina - I suspect there's some misregistration, or part of the brain mask (and hence the anatomical segmentation) missing or something like that. Do you mind uploading the tracula directories of this subject for me to take a look at? https://gate.nmr.mgh.harvard.edu/filedrop2/

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

You get the same error as trac-all because trac-all runs mri_convert. I'd send the mri_convert error in a new email with mri_convert somewhere in the title, so that someone else can help you. On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Also when I run mir_convert on the DICOMs I get the

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

Also when I run mir_convert on the DICOMs I get the same error as the one I got when I used DICOMs : WARNING: file /Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized?

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

It says 1 … I don’t understand why I get that knowing that when I open the nifti I can go through the frames … Ismail > On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki > wrote: > > > I do not know why the dicoms do not work. When you run mri_info on your >

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

I do not know why the dicoms do not work. When you run mri_info on your nifti, what is the number of frames that shows up? On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So this shouldn’t be the reason.

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

Hi Anastasia, This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So this shouldn’t be the reason. Also why the DICOMs wouldn’t work at the beginning ? Thanks, Ismail > On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki > wrote: > > > Hi

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

Hi Ismail - You can see from the log file that the command that causes the error is this: mri_convert --frame 31 /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz It's trying to extract the 32nd

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

Hi Anastasia, Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again, Ismail > On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki > wrote: > > > Hi Ismail - It sounds like the error has to

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

Hi Ismail - It sounds like the error has to do with the nifti volume, not the bvecs/bvals. Can you send the log file from scripts/trac-all.log? Thanks, a.y On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more. I run trac-all -prep -c on some DICOM files but I had the following error : WARNING: file

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file. Best, a.y On Tue, 28 Jun 2016, Koubiyr, Ismail wrote: > Hi everyone, > > I have some problems trying to run TRACULA on some DWI data. It is a mosaic > Siemens DWI.

[Freesurfer] Tracula : ERROR: cannot unpack mosiacs without ASCII header

Hi everyone, I’m reposting my problem if someone could help me I would really appreciate it. I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c

[Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not

Re: [Freesurfer] TRACULA error related to bvec/bval input

Hi Scott - The gradient table produced by dcm2nii is formatted in 3 rows, rather than 3 columns. If you want to use gradient tables formatted in rows, you have to download the tracula update described here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates a.y On Tue, 7 Apr

[Freesurfer] TRACULA error related to bvec/bval input

Hi,I am trying to get TRACULA running. I have converted the DTI data using dcm2nii (as i was unable to get tracula to read the .ima Siemens DICOM) and have a bevc and bval file output from dcm2nii.The error I get is in bold below (from trac-all.log). I believe that the error is coming from the

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