Re: [Freesurfer] Error message when creating a stats table

External Email - Use Caution Dear Freesurfer team, I already found the error. Kind regards, Rosie On Mon, Jul 5, 2021 at 3:31 PM Rosalia Dacosta Aguayo wrote: > Dear Freesurfer team, > > I am having the following error message when I try to run the stats table: > > rosalia@

[Freesurfer] Error message when creating a stats table

External Email - Use Caution Dear Freesurfer team, I am having the following error message when I try to run the stats table: rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI/FREESURFER_CAN_RUTI $ asegstats2table --subjects sub-002_ses-BSL sub-003_ses-BSL sub-004_ses-BSL sub

Re: [Freesurfer] error message when running mri_info

You can see that the vox_units are Unknown in the fslhd output. This is the source of the problem in FS. On 12/18/2020 10:53 AM, Jonathan Lynn wrote: External Email - Use Caution Hello, I've been using a software to process SWI data that includes an option to save the output as nifti

[Freesurfer] error message when running mri_info

External Email - Use Caution Hello, I've been using a software to process SWI data that includes an option to save the output as nifti files. When I attempt to use either the mri_info or mri_convert commands on these nifti files I receive the following error message: niiRead():

[Freesurfer] error message {Disarmed}

External Email - Use Caution Dear Freesurfer team, I'm running a group analysis where I'd like to compare myelination between two groups regressing out cortical thickness, age and sex. My FSGD file is: GroupDescriptorFile 1 Title Func Class HC Class CMT Variables Age gender Input

Re: [Freesurfer] error message using mri_robust_template

Best, Marisa Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Martin Reuter Gesendet: Freitag, 18. September 2020 13:27 An: Freesurfer support list Betreff: Re: [Freesurfer] error message using mri_robust_template Hi Marisa, the main go

Re: [Freesurfer] error message using mri_robust_template

Hi Marisa, the main goal of robust_template is to remove rigid motion between scans. So the first question is, do you really need (want) affine? The next question is, if this still occurs in FS 7.1.1 I remember dimly that I worked on this some years ago (basically allow a larger threshold, as

[Freesurfer] error message using mri_robust_template

External Email - Use Caution Hello, I am using mri_robust_template with the ‘--affine’ option to create individual templates (using freesurfer version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). For each timepoint I use that timepoint's T1.mgz as the input. For s

Re: [Freesurfer] Error message when using mri_glmfit-sim "ERROR: could not open .csd"

And one more thing, I noticed that you were using a cluster forming threshold of 1.3 (p<.05). This low a threshold is not recommended when using mc-z (you can use it with permutation, which is more generally recommended) On 8/25/2020 12:18 PM, Diógenes Diego wrote: External Email -

Re: [Freesurfer] Error message when using mri_glmfit-sim "ERROR: could not open .csd"

oh, wait, I do see the error in there now, but it did not appear to cause the program to fail. I tracked down and fixed the problem. It should not actually create any issues for your output, so you can just ignore the error. On 8/25/2020 12:18 PM, Diógenes Diego wrote: External Email

Re: [Freesurfer] Error message when using mri_glmfit-sim "ERROR: could not open .csd"

That file was apparently not created when running mri_glmfit-sim, but the log files did not show an error On 8/25/2020 12:18 PM, Diógenes Diego wrote: External Email - Use Caution What is the reason for this message? ERROR: could not open lh.volume.example.10.glmd/csd/all.cache.th13

Re: [Freesurfer] Error message when using mri_glmfit-sim "ERROR: could not open .csd"

External Email - Use Caution What is the reason for this message? ERROR: could not open lh.volume.example.10.glmd/csd/all.cache.th13.pos-CONTROLE-PK.csd Thanks Diogenes Bispo > Em 25 de ago de 2020, à(s) 12:22, Douglas N. Greve > escreveu: > >  It does not look like any o

Re: [Freesurfer] Error message when using mri_glmfit-sim "ERROR: could not open .csd"

It does not look like any of those have errors? On 8/25/2020 8:56 AM, Diógenes Bispo wrote: External Email - Use Caution Here follows the screen capture for the --debug option within the commands. Really appreciate all the help. Sincerely. Diógenes Bispo diogenesdi...@gmail.com

Re: [Freesurfer] Error message when using mri_glmfit-sim "ERROR: could not open .csd"

There was nothing attached, but  the summary is probably not too helpful. Can you run it again with --debug as the first option. Capture the terminal output in a file and send it in. On 8/22/2020 5:04 PM, Diógenes Bispo wrote: External Email - Use Caution Hi Freesurfer Community, I'm

[Freesurfer] Error message when using mri_glmfit-sim "ERROR: could not open .csd"

External Email - Use Caution Hi Freesurfer Community, I'm using Freesurfer for the volumetric analysis of Parkinson's patients in comparison with a control group. While trying to execute it for a sample of 6 patients (3 from each group), I got one error during the mri_glmfit-sim. I

Re: [Freesurfer] error message while using autorecon1

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Sent: Wednesday, July 05, 2017 2:30 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1 I ran "which nu_correct" and it says command no

Re: [Freesurfer] error message while using autorecon1

urfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hoopes, Andrew Sent: Wednesday, July 05, 2017 2:05 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1 After sourcing freesurfer, what comes up if you run the command "which nu_co

Re: [Freesurfer] error message while using autorecon1

on behalf of Buckless, Colleen Sent: Wednesday, July 05, 2017 1:36 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] error message while using autorecon1 Hi Andrew, The output list includes nu_correct. Thanks, Colleen -Original Message- From: freesurfer-boun...

Re: [Freesurfer] error message while using autorecon1

7; Subject: Re: [Freesurfer] error message while using autorecon1 Hi Colleen, If you source freesurfer, and run: ls $FREESURFER_HOME/mni/bin It should output a list of mni tools, including nu_correct. Is this what you see? There's a possibility that your mni sub-directory isn&#x

Re: [Freesurfer] error message while using autorecon1

urfer-boun...@nmr.mgh.harvard.edu on behalf of Buckless, Colleen Sent: Wednesday, July 05, 2017 12:18 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: [Freesurfer] error message while using autorecon1 Hi All, I am using the newest version of freesurfer, and I keep getting errors w

[Freesurfer] error message while using autorecon1

Hi All, I am using the newest version of freesurfer, and I keep getting errors when I run recon-all -autorecon1. It appears that the error might have to do with nu_correct, and I have attached the recon-all.log. Any suggestions on how to fix this? Thanks, Colleen Buckless Research Assistant Cent

Re: [Freesurfer] Error message

Hi Lawrence can you send us the full command line and screen output of what you ran? thanks Bruce On Wed, 11 Jan 2017, shi yao wang wrote: Dear FS teams:  when I running FS, there is a message like this:  Error:Cannot find CTF archive /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimate

[Freesurfer] Error message

Dear FS teams: when I running FS, there is a message like this: Error:Cannot find CTF archive /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf Is it a real Error message? Cause, it seems that the recon -all process successfully finished. thanks Lawrence ___

Re: [Freesurfer] Error message with lh.BA1.label

Ok, i actually think it would be easier to have only one FS version. How could i get the BA labels (and all the other coontents of fsaverage) again? Best, Max On dijous 19 novembre 2015 15:51 CET, Bruce Fischl wrote: > yes, that's pretty much it. Alternatively we could just give you a

Re: [Freesurfer] Error message with lh.BA1.label

yes, that's pretty much it. Alternatively we could just give you all the current BA labels and the command lines need to run to map them from fsaverage to your subjects On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote: Dear Bruce, Thank you, I will try to do that, but I am

Re: [Freesurfer] Error message with lh.BA1.label

Dear Bruce, Thank you, I will try to do that, but I am not so clear about it. I should install the 6.0beta version of FS, but keep the one I have currently (v 1.379.2.73)? Then I should run with the 6.0beta version recon-all -balabels -i /path/to/file -s subjid; and then the complete recon-al

Re: [Freesurfer] Error message with lh.BA1.label

that means the FS version you have didn't have those labels. We can get you the entire set of BA labels, but you will need a new version of recon-all. Maybe your best bet is to insteall 6.0 beta and just run the -balabels target from it? On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU V

Re: [Freesurfer] Error message with lh.BA1.label

Dear Bruce, # ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label ls: Kein Treffer. (meaning: no match) # ls /usr/local/freesurfer/subjects/fsaverage ls: Zugriff auf /usr/local/freesurfer/subjects/fsaverage nicht möglich: Zu viele Ebenen aus symbolischen Links (meaning: access to /us

Re: [Freesurfer] Error message with lh.BA1.label

Can you run: ls /usr/local/freesurfer/subjects/fsaverage/label/*BA1*.label and report the results? cheers Bruce On Thu, 19 Nov 2015, BAUTISTA-PERPINYA Maximilia (ETU VIE) wrote: Dear all, I get the same error when running any subject. I think it may be related to the step concerning: fs

[Freesurfer] Error Message when Accessing Bin

Hello, When I run the command "sFSstart" on version 5.0.0, I am receiving the messages below. Would you please explain to me what the problem is? It seems like there is trouble accessing the bin. Thank you freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 Setting up environment f

Re: [Freesurfer] error message recon-all

Hi Lars you have to give recon-all some directive telling it what to do (-all, -autorecon1, -autorecon2, -autorecon3). cheers Bruce On Thu, 22 Jan 2015, Lars M. Rimol wrote: Hi, I keep getting this error message when running, or trying to run, recon-all. I suspect there is a file somewher

[Freesurfer] error message recon-all

Hi, I keep getting this error message when running, or trying to run, recon-all. I suspect there is a file somewhere indicating that this subject has been run before. But all that is in the directory 3002 is dicom images. What is wrong? [LMR in subjects/DTI ] recon-all -subjid 3002 -i 3002/1.dcm E

Re: [Freesurfer] Error message

..@hotmail.com > Subject: Re: [Freesurfer] Error message > > Muhammed, > > In the email below you state recon-all exited with errors. But in the > recon-all.log file you sent me, there is no error message. I need the > recon-all.log that contains the error for the subject you a

Re: [Freesurfer] Error message

d.edu; mniqure...@hotmail.com > Subject: Re: [Freesurfer] Error message > > Muhammad, > > Please send me the recon-all.log file for this subject. It should be > found in: > > /media/sf_Dataset/ADHD200/Processed/scripts/recon-all.log > > Thanks. > > -Zeke > &g

Re: [Freesurfer] Error message

Muhammad, Please send me the recon-all.log file for this subject. It should be found in: /media/sf_Dataset/ADHD200/Processed/scripts/recon-all.log Thanks. -Zeke On 01/04/2015 07:56 PM, Muhammad Naveed Iqbal Qureshi wrote: > Dear community, > > I execute the following command: > > recon-all -i

Re: [Freesurfer] Error Message

; > > > > > > > > > > > > echo "Iteration $nthIter `date`" | & tee -a $LF > > > > > > > echo Iteration 1 `date` > > > > > > > tee -a ./mri_

Re: [Freesurfer] Error Message

nc -tmpdir > > > > > ./tmp.mri_nu_correct.mni.14983/0/ -iterations 1000 ) > > > > > if ( $#StopThresh ) set cmd = ( $cmd -stop $StopThresh ) ; > > > > > if ( 0 ) set cmd = ( nu_correct -clobber > > > > > ./tmp.mri_nu_correct.mni.14983/nu0.mnc

Re: [Freesurfer] Error message

always listen to Doug instead of me :) On Sun, 4 Jan 2015, Douglas Greve wrote: Can you run cd /media/sf_Dataset/ADHD200/Processed/mri  mri_nu_correct.mni --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz |& tee dng.log and send me dng.log doug On 1/4

Re: [Freesurfer] Error message

Hi Muhammad can you send us the file /media/sf_Dataset/ADHD200/Processed/scripts/recon-all.log thanks Bruce On Mon, 5 Jan 2015, Muhammad Naveed Iqbal Qureshi wrote: Dear community,   I execute the following command:   recon-all -i/media/sf_Dataset/ADHD200/adhd_200/Brown_26001/Brown_26001_1

Re: [Freesurfer] Error message

Can you run cd /media/sf_Dataset/ADHD200/Processed/mri mri_nu_correct.mni --debug --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz |& tee dng.log and send me dng.log doug On 1/4/15 7:56 PM, Muhammad Naveed Iqbal Qureshi wrote: Dear community, I execute the

[Freesurfer] Error message

Dear community, I execute the following command: recon-all -i /media/sf_Dataset/ADHD200/adhd_200/Brown_26001/Brown_26001_1/scans/anat_1-anat/resources/NIfTI/files/rest.nii.gz -subject /media/sf_Dataset/ADHD200/adhd_200/Brown_26001/Brown_26001_1/scans/anat_1-anat/resources/NIfTI/files/Proces

Re: [Freesurfer] Error message of Ubuntu 13.04 and Centos4 & Centos6

I had a similar error when using CentOS on VirtualBox. The error came from an error in the OpenCL driver. Are you running a virtualmachine? If not i would advise trying a different graphics driver. As to the CentOS/Ubuntu choice. I would go with CentOS as it seems more stable/constant and is more e

Re: [Freesurfer] Error message of Ubuntu 13.04 and Centos4 & Centos6

JoJo, I have not tried to recreate your issues on machine running Ubuntu 13.04 but have tried to run the commands on Ubuntu 12.04. To summarize: 1) Regarding your first issue... this is standard output to the terminal on certain OS's including Ubuntu. I got it when I tested your command but th

[Freesurfer] Error message of Ubuntu 13.04 and Centos4 & Centos6

Dear Freesurfer experts, I installed FS Centos4-64(and also tried Centos6) on Ubuntu 13.04. I followed the commands in tutorial and got error message, listed as follows. (Nevertheless, FS can read in volume and surface from GUI.) Another question is, which one of Centos4 or Centos6 is more sui

[Freesurfer] Error message of Ubuntu 13.04 and Centos4 & Centos6

Dear Freesurfer experts, I installed FS Centos4-64(and also tried Centos6) on Ubuntu 13.04. I tried the commands in tutorial and got error message, listed as follows. Nevertheless, FS can read in volume and surface from GUI. Another question is, which one of Centos4 or Centos6 is more suitab

[Freesurfer] error message with crStateSetCurrentPointers() in your SPU

Hi Everyone, I installed Freeview on Ubuntu 10.04 and the program kind of works but I get this error message when I'm running the program. OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU What happens is that when I try and load a file, it disappears behind the bla

Re: [Freesurfer] Freesurfer-Error message

vard.edu/fswiki/BugReporting > > FreeSurfer:~/freesurfer/subjects/test1> > > -Original Message- > From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] > Sent: Dienstag, 4. September 2012 18:25 > To: Varghese, Chikku > Subject: Re: [Freesurfer] Freesurfer-Error messag

Re: [Freesurfer] Freesurfer-Error message

Thanks Bruce, Still no luck,this what I am getting /freesurfer/subjects/test1> recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid test7 -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INF

Re: [Freesurfer] Freesurfer-Error message

Hi Chikku you need to give it the path to an image file (any one will do) and it will figure out the other slices that makeup the same series. What is the resolution of your data? 50 slices isn't usually enough to cover the brain at high enough resolution to get good thickness results. cheer

[Freesurfer] Freesurfer-Error message

Hi, While running the following command: recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre -subjid test2 I keep seeing the following error: ... corRead(): can't open file /media/sf_freesurferstudys/raw/raw_scr/T1pre/COR-.info $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp

Re: [Freesurfer] error message for recon-all

Thank you so much Bruce, it now works like a charm! Best, Muriel On Jul 12, 2012, at 2:30 AM, Bruce Fischl wrote: > Hi Muriel > > not sure what your second frame is, but you should be able to do this: > > cd $SUBJECTS_DIR//mri/orig > mv 001.mgz multiframe.mgz > mri_convert -nth 0 multiframe.m

Re: [Freesurfer] error message for recon-all

you can run freeview on the 001.mgz and see what is in it. If it has more than one frame freeview will include a slider that lets you change from one to the other. Or you can email it to me and I'll take a look. On Wed, 11 Jul 2012, Muriel Bruchhage wrote: > Hi Bruce, > > To be quite honest, I

Re: [Freesurfer] error message for recon-all

Hi Bruce, To be quite honest, I am not sure, but I used the same data on a fsl segmentation task (using a nifti format though) and I never got any error messages back there. Best, Muriel On Jul 11, 2012, at 11:26 PM, Bruce Fischl wrote: > Hi Muriel > > what was the scan that you are trying t

Re: [Freesurfer] error message for recon-all

Hi Muriel what was the scan that you are trying to run FreeSurfer on? Did it have more than one echo? Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: > > On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote: > >> I added the -all at the end and skipped the -i flag, but I still get an >>

Re: [Freesurfer] error message for recon-all

On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote: > I added the -all at the end and skipped the -i flag, but I still get an error > message: > > Checking for (invalid) multi-frame inputs... > ERROR: input(s) cannot have multiple frames! > /Applications/freesurfer/subjects/MRI_04_2012/GID02/

Re: [Freesurfer] error message for recon-all

oh, you need to specify what you want it to do. Add -all at the end of the command line and it will do everything. Note that if you are rerunning, you can leave out the -i cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: > Hei, > > Thanks you very much again for your help! > > Neve

Re: [Freesurfer] error message for recon-all

Hei, Thanks you very much again for your help! Nevertheless, even though I got the message that the recon-all has been done without any errors, no talaraich transform, skull stripping or segmentation has been done. I placed my fsaverage folder in the same folder where all my participant-folde

Re: [Freesurfer] error message for recon-all

sure, glad it worked out Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: > > It worked! > > Thank you so so much! > > Best, > Muriel > > On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: > >> Hi Bruce, >> >> Thank you very much for your fast response. >> >> Unfortunately though, I still get

Re: [Freesurfer] error message for recon-all

It worked! Thank you so so much! Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: > Hi Bruce, > > Thank you very much for your fast response. > > Unfortunately though, I still get an error response when typing in "recon-all > -i /Applications/freesurfer/subjects/MRI_04_2012

Re: [Freesurfer] error message for recon-all

Hi Muriel the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i . And one acquisition is usually suffi

[Freesurfer] error message for recon-all

Hi, I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance). What I have been done so far: 1) I set my Freesurfer environment in my .tcshrc file to: setenv FREESURFER_HOME /Applications/freesurfer/ source $FRE

Re: [Freesurfer] error message in tkmedit

Hi Rashmi why do you include $FREESURFER_HOME/FreeSurferColorLUT.txt on the command line? I think you can just remove it and you will be fine cheers Bruce On Wed, 1 Feb 2012, Rashmi Singh wrote: While opening tkmedit using terminal I gave following command  % crick:~/storage/labs/pbellgow

[Freesurfer] error message in tkmedit

While opening tkmedit using terminal I gave following command % crick:~/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/FreeSurfer> tkmedit AA471.T0 brainmask.mgz -aux T1.mgz -segmentation aseg.mgz -surfs $FREESURFER_HOME/FreeSurferColorLUT.txt The output was Converting main surface: 100% done. Conv

Re: [Freesurfer] Error message for getting the stat file into table format

Did you look at the file to see if it looks reasonable? Eg, it might be completely empty if you ran out of space during the processing. doug Rashmi Singh wrote: > Hello, > I was trying to get the cortical thickness in the table format for > all of my subjects on which I had run recon all. I se

Re: [Freesurfer] Error message for getting the stat file into table format

Hi Rashmi, Could you check that the ?h.aparc.stats for the subjects exist and contain actual measurements? If not, check the /scripts/recon-all.log to see if the -parcstats step failed. Also, double-check your SUBJECTS_DIR path is correct. -Louis On Wed, 25 Jan 2012, Rashmi Singh wrote: > Hel

[Freesurfer] Error message for getting the stat file into table format

Hello, I was trying to get the cortical thickness in the table format for all of my subjects on which I had run recon all. I see the stats folder with rh/lh.aparc.stats files. My command was: aparcstats2table --subjects AA471.T1 AA471.T2 AA471.T3 AA474.T0 AA476.T0 AA479.T0 AA483.T0 AA483.T2 AA

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

[gr...@nmr.mgh.harvard.edu] Sent: Friday, October 21, 2011 12:22 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3 The BA labels should be in $FREESURFER_HOME/subjects/fsaverage/label doug Vy Dinh wrote: &

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Email: vy_d...@rush.edu > > > From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] > Sent: Friday, October 21, 2011 9:51 AM > To: Vy Dinh > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & > autorecon3 &g

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Dinh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3 So the BA labels don't exist in $FREESURFER_HOME/subjects/fsaverage/label? What version are you using? doug Vy Dinh wrote: > You're absolutely right. The

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Rush University Medical Center > Phone: (312) 563-3853 > Fax: (312) 563-4660 > Email: vy_d...@rush.edu > > > From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] > Sent: Thursday, October 20, 2011 1:10 PM > To: Vy Dinh > Cc: fr

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

nh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3 No, it means that it cannot find that file. doug Vy Dinh wrote: > Then does it mean that I can ignore this error message? > > Vy T.U. Dinh > Research As

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Email: vy_d...@rush.edu > > > From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] > Sent: Thursday, October 20, 2011 12:51 PM > To: Vy Dinh > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Freesurfer Error Message in running auto

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

...@nmr.mgh.harvard.edu] Sent: Thursday, October 20, 2011 12:51 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3 It does need to be there, but usually it creates it's own symbolic link (so you should not need to copy it).

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

las N Greve [gr...@nmr.mgh.harvard.edu] > Sent: Thursday, October 20, 2011 12:26 PM > To: Vy Dinh > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & > autorecon3 > > Does /Users/subdir/ fsaverage exist? Also

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

...@rush.edu From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, October 20, 2011 12:26 PM To: Vy Dinh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3 Does /Users/su

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Does /Users/subdir/ fsaverage exist? Also, it looks like there could be a space between "subdir/" and "fsaverage" doug Vy Dinh wrote: > Dear Experts, > > I ran the wm.mgz corrections and pial corrections using the command: > > -autorecon2 –autorecon3 –subjid sub2 > > However, Freesurfer exite

[Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Dear Experts, I ran the wm.mgz corrections and pial corrections using the command: -autorecon2 –autorecon3 –subjid sub2 However, Freesurfer exited the program with the following message: SUBJECTS_DIR/Users/subdir FREESURFER_HOME Applications/freesurfer Loading source label. No such file or

[Freesurfer] error message from fast_selxavg.m

Hi, I was running selxavg-sess, and met this error: >> >> >> >> >> >> $Id: fast_selxavg.m,v 1.40.2.2 2009/04/09 20:01:57 greve Exp $ Parsing Arguments RescaleTarget = 1000 UseMRIread = 1, ext = nii Checking Parameters ??? Undefined function or variable "xyzscale". Error in ==> load_nifti_hdr at

Re: [Freesurfer] error message in mri_concat: fp==0

stacksize 10240 kbytes, sorry! -- yours, Dr. Lars M. Rimol ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom

Re: [Freesurfer] error message in mri_concat: fp==0

cputime,filesize,datasize,memoryuse,vmemoryuse: unlimited stacksize 10240 bytes coredumpsize 0 kbytes descriptors 1024 memorylocked 32 kbytes maxproc 137216 yours, LMR On 20/01/2011, Bruce Fischl wrote: > I see. Maybe there are too many open file descriptors? If you type 'limit' > what does it t

Re: [Freesurfer] error message in mri_concat: fp==0

I see. Maybe there are too many open file descriptors? If you type 'limit' what does it tell you? On Thu, 20 Jan 2011, Lars M. Rimol wrote: > Hi Bruce, > > Yes I can create files. I was trying to run a script with almost 500 > mgh files that I wanted to concatenate. I figured there was somethin

Re: [Freesurfer] error message in mri_concat: fp==0

Hi Bruce, Yes I can create files. I was trying to run a script with almost 500 mgh files that I wanted to concatenate. I figured there was something wrong with the script because I could run command lines to concatenate 10-20 files from that list in the terminal (all 500 files was too much to copy

Re: [Freesurfer] error message in mri_concat: fp==0

Hi Lars do you have write permission? Is the partition full? Try: touch /home/lmr/test.mgh and see if that works cheers Bruce On Thu, 20 Jan 2011, Lars M. Rimol wrote: > Hi, > > I got this error message when attempting to use mri_concat. Number or > inputs, frames etc. seems ok, but when

[Freesurfer] error message in mri_concat: fp==0

Hi, I got this error message when attempting to use mri_concat. Number or inputs, frames etc. seems ok, but when it is about to write the output file, this happens: Writing to /home/lmr/test.mgh , -1): could not open file: fp==0 (I use v.4.5.0) Any suggestions? Thank you! yours, LMR -- yo

[Freesurfer] Error message in opening OSX 10.5 version image disk of FS

Hi there, I'm using a Mac OS X 10.6.3. I tried to install the freesurfer-Darwin-leopard-i686-stable-pub-v4.5.0-full.dmg but I'm not allowed/able to open it, getting the error message "invalid checksum". Is it something up to the image disk version (i.e. do I need to use a *v4.6.3-full.dmg image?)

Re: [Freesurfer] error message on "make_average_volume"

sorry, i meant to say include the --no-aseg flag with make_average_volume (make_average_subject is just a wrapper script that calls make_average_volume and make_average_surface). n. On Wed, 2010-01-27 at 14:02 +0800, lordowen wrote: > Hi: > > Thank you for your replies. But how I can including

Re: [Freesurfer] error message on "make_average_volume"

Hi: Thank you for your replies. But how I can including the flag? According to wiki there is no such optional argument in mark_average_subject, and adding "--no-aseg" did not work. Can you advise me in more detail? Thank you for your kindness help. 2010/1/26 Nick Schmansky : > try including the

Re: [Freesurfer] error message on "make_average_volume"

try including the -no-aseg flag with make_average_subject. this out-of-memory error is a known issue, that only has this work-around. for other known-issues, see: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes On Tue, 2010-01-26 at 17:16 +0800, lordowen wrote: > Dear freesurfer expertise:

Re: [Freesurfer] error message on "make_average_volume"

probably not enough RAM. How much memory is in the machine? Bruce On Tue, 26 Jan 2010, lordowen wrote: > Dear freesurfer expertise: > > When I perform the make_average_subject to obtain the custom average > template, I encountered following error message in make_average_volume > step: > > L

[Freesurfer] error message on "make_average_volume"

Dear freesurfer expertise: When I perform the make_average_subject to obtain the custom average template, I encountered following error message in make_average_volume step: Loading mask /usr/local/freesurfer/subjects/avgsubject/mri/brainmask.mgz ninput = 64 Chcking inputs Checking 0 /usr/loca

Re: [Freesurfer] Error message

what does the file transforms/talairach_avi.log say? On Wed, 2009-10-07 at 10:05 -0400, Weisinger, Brian (NIH/OD) [E] wrote: > This error message came up when running the base run with the notal > check...any ideas how to fix this problem? > > imgrege: no voxels in register > ERROR: 'imgreg_4df

[Freesurfer] Error message

This error message came up when running the base run with the notal check...any ideas how to fix this problem? imgrege: no voxels in register ERROR: 'imgreg_4dfp /Applications/freesurfer/average/711-2C_as_mni_average_305 /Applications/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g

Re: [Freesurfer] Error message running recon-all-base

Only to the runs, where the check fails (if the transform looks OK). So in your case the -base run. Good luck, Martin On Mon, 2009-10-05 at 10:01 -0400, Weisinger, Brian (NIH/OD) [E] wrote: > When you said to process it with the -notal-check to skip the talairach > checkam I supposed to add

Re: [Freesurfer] Error message running recon-all-base

When you said to process it with the -notal-check to skip the talairach checkam I supposed to add that in the first recon all or add it to the recon all base command? On 10/2/09 1:15 PM, "Martin Reuter" wrote: Looks like the talairach check failed. Check the talairach.xfm (as you would do

Re: [Freesurfer] Error message running recon-all-base

How exactly do I check the talairach.xfm? Are there instructions somewhere? I looked at the subjects brains with tkmedit, tksurfer and they look fine. On 10/2/09 1:15 PM, "Martin Reuter" wrote: Looks like the talairach check failed. Check the talairach.xfm (as you would do in the cross section

Re: [Freesurfer] Error message running recon-all-base

Looks like the talairach check failed. Check the talairach.xfm (as you would do in the cross sectional processing, when this happens -> tutorial). If it looks OK try processing with -notal-check to skip the check. If it looks wrong, try to correct it with tkregister manually. Sometimes the transfor

[Freesurfer] Error message running recon-all-base

I was running recon-all -base Sub1 -tp 00308 -tp 01150 -all After a couple of minutes it gave me this error message. Fri Oct 2 09:48:05 EDT 2009 talairach_avi done \n cp transforms/talairach.auto.xfm transforms/talairach.xfm \n # #...@# Talairach

Re: [Freesurfer] Error message starting qdec analysis

Rosa, I'm not sure, but the last time someone wrote about this error message, the problem was that they had more than 2 levels for one of their factors. By any chance, did you have more than two for the factor you included in these designs? -- On Mon, 6 Jul 2009, Rosa Steimke wrote: HI! W

[Freesurfer] Error message starting qdec analysis

HI! When I sart the qdec analysis an error message comes up at around 70%. The error message says: Error in Analyze: command failed: mri_glmfit —y/Users/.../qdec/alh/y.mgh —fsgd /Users/.../qdec/alh/qdec.fsgd dods —glmdir /Users/.../qdec/alh —surf fsaverafe lh —label /Users/.../fsaverage/label/lh.

RE: [Freesurfer] error message

; Freesurfer Mailing List Subject: RE: [Freesurfer] error message Fatima, Can you send me the output of this command: env | grep PERL Nick On Mon, 2009-06-22 at 09:56 +0200, Ahmed, F, Me wrote: > Nick, > > I tried running fixup_mni_paths and got the following output (see attached). &g

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