Re: [Freesurfer] Cannot allocate memory

Hi Gabriel they are in the subject's directory. Have you gone through the FS tutorials on our wiki? That would be a good place to start cheers Bruce On Tue, 25 Feb 2020, Gabriel Tapia wrote: External Email - Use Caution Hello Bruce thank you for your quick reply, Where

Re: [Freesurfer] Cannot allocate memory

External Email - Use Caution They are all in the output folder of the subject. The noxfix files are surfaces (in /surf/), the mgz file is a volume (in /mri/). Tim > On February 25, 2020 at 4:24 AM Gabriel Tapia wrote: > > > External Email - Use Caution > >

Re: [Freesurfer] Cannot allocate memory

External Email - Use Caution Hello Bruce thank you for your quick reply, Where should I look to get all these files? The idea to check them is to confirm that the MRI went wrong at some point, right? Thanks, Gabriel Tapia www.Partage3D.fr

Re: [Freesurfer] Cannot allocate memory

Hi Gabriel, that is a huge defect and generally means something major has gone wrong. Look at the lh or rh.orig.nofix and the corresponding ?h.inflated.nofix over the wm.mgz file to see what is wrong (usually something like a big chunk of skull is left over and connected to the surface,

[Freesurfer] Cannot allocate memory

External Email - Use Caution Hello dear Freesurfer developers, nice to e-meet you and thank you for working on this open source software! I am trying to produce a 3D file of a brain. The command I am trying to run is recon-all and here is the error I get: *CORRECTING DEFECT 57

Re: [Freesurfer] Cannot allocate memory error

Hi Aziz freeview is the tool for visualizing the data, so use it to examine the outputs of recon-all and figure out what is causing the big defect cheers Bruce On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: Hi Bruce, So, I  should run the freeview after got those error messages. I will

Re: [Freesurfer] Cannot allocate memory error

Hi Bruce, So, I should run the freeview after got those error messages. I will try. Thank you, Aziz. On Thu, Jan 12, 2017 at 10:32 PM, Bruce Fischl wrote: > Hi Aziz > > it will be in the subject's surf dir. You can visualize it via: > > freeview -f

Re: [Freesurfer] Cannot allocate memory error

Hi Aziz it will be in the subject's surf dir. You can visualize it via: freeview -f $SUBJECTS_DIR//surf/lh.inflated.nofix cheers Bruce On Thu, 12 Jan 2017, Aziz Nanthaamornphong wrote: Hi Bruce, How can I look at inflated.nofix as you mentioned? I think I ran recon-all for the 001.mgz

Re: [Freesurfer] Cannot allocate memory error

Hi Bruce, How can I look at inflated.nofix as you mentioned? I think I ran recon-all for the 001.mgz without other files. Best Regards, Aziz. On Thu, Jan 12, 2017 at 8:55 PM, Bruce Fischl wrote: > Hi Aziz > > yes, you ran out of RAM. That said, a defect with 66K

Re: [Freesurfer] Cannot allocate memory error

Hi Aziz yes, you ran out of RAM. That said, a defect with 66K vertices is pretty big - more than 1/3 of a typical surface. You should check to make sure nothing big is wrong (hemis attached, skull left around, etc). Look at the inflated.nofix surface and it should be obvious what the

[Freesurfer] Cannot allocate memory error

Hi experts, I ran the command $recon-all -all -subjid 0696 I have got these error messages *CORRECTING DEFECT 46 (vertices=66623, convex hull=8931)* *Excessive topologic defect encountered: could not allocate 322592700 edges for retessellation* *Cannot allocate memory* *Linux

Re: [Freesurfer] Cannot allocate memory mri_glmfit to remove covariates

Thanks Douglas, it works now! On Thu, Aug 25, 2016 at 6:45 AM, Douglas N Greve wrote: > It actually looks like it might be a problem with your covariates.mat > file (MatrixReadTxT error). Can you send that file? > > > On 08/22/2016 10:06 PM, Heidi Foo wrote: > > Dear

Re: [Freesurfer] Cannot allocate memory mri_glmfit to remove covariates

It actually looks like it might be a problem with your covariates.mat file (MatrixReadTxT error). Can you send that file? On 08/22/2016 10:06 PM, Heidi Foo wrote: > Dear FreeSurfer team, > > I am currently running mri_glmfir --eres-save using FreeSurfer 6.0. > However, there is an error saying

Re: [Freesurfer] cannot allocate memory

Hi Doug, Thanks. I was wondering if you think this would do the job: 1) use fmcpr.nii.gz 2) split it to 3d volumes 3) do mri_vol2vol for all the volumes separely 4) concatenate the resampled volumes together to get a 4d volume. If you don't think this is a good approach, I appreciate it if

Re: [Freesurfer] cannot allocate memory

The problem is not the command, it is the size of the data it generates. You can try reducing the size of the anatomical to a bounding box around the brain. This is a bit tricky as you also have to compute a new registration. I can help step you through the process if you want to go in that

Re: [Freesurfer] cannot allocate memory

Hi Doug, Thanks for your response. What I'm trying to do is to get each voxel's times course in structural space and I was under the impression that mri_vol2vol --mov func.nii would be the right way to go. Would you please let me know what the best way would be to do this? best, Ehsan,. On

Re: [Freesurfer] cannot allocate memory

that's going to create a pretty big volume as it will map your functional time course to a 256^3 float volume. If you have 100 time points, then that will be about 7G. On 3/16/16 3:27 PM, Ehsan Tadayon wrote: Hi Bruce, Thanks for your response. I'm using : freesurfer version:

Re: [Freesurfer] cannot allocate memory

Hi Bruce, Thanks for your response. I'm using : freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on OS X Yosemite 10.10.5 with 16 GB 1333 MHz DDR3 memory. The command that I'm using: mri_vol2vol --mov func.nii.gz --fstarg --reg register.dat --o func.anat.nii.gz Thanks in

Re: [Freesurfer] cannot allocate memory

Hi Ehsan We need the full command line and screen output and also what your hardware and software environments are to help you. Certainly sounds like you ran out of memory though Cheers Bruce > On Mar 15, 2016, at 11:41 PM, Ehsan Tadayon wrote: > > Ehsan

[Freesurfer] cannot allocate memory

Dear Freesurfer experts, I'm trying to run mri_vol2vol on a functional mri to resample it onto orig.mgz. I get this error: ``` mri_vol2vol(98217,0xa0ce01d4) malloc: *** mach_vm_map(size=262144) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to

Re: [Freesurfer] Cannot allocate memory

] Gesendet: Montag, 12. Mai 2014 15:44 An: Freesurfer support list Betreff: Re: [Freesurfer] Cannot allocate memory Hi Kristina you need to give us more context. What command is running when you get that error? cheers Bruce On Mon, 12 May 2014, Mayer Kristina wrote: Hi there, I am

[Freesurfer] Cannot allocate memory

Hi there, I am using freesurfer on MRI data of children. In one dataset I have following error appearing, I did not find described before. MRISalloc(41043678, 76): could not allocate faces Cannot allocate memory Linux cs2.kispi.int 3.13.5-103.fc19.x86_64 #1 SMP Mon Mar 3 18:46:36 UTC 2014

Re: [Freesurfer] Cannot allocate memory

Hi Kristina you need to give us more context. What command is running when you get that error? cheers Bruce On Mon, 12 May 2014, Mayer Kristina wrote: Hi there, I am using freesurfer on MRI data of children. In one dataset I have following error appearing, I did not find described

Re: [Freesurfer] Cannot allocate memory

] Cannot allocate memory Hi Kristina you need to give us more context. What command is running when you get that error? cheers Bruce On Mon, 12 May 2014, Mayer Kristina wrote: Hi there, I am using freesurfer on MRI data of children. In one dataset I have following error appearing, I did

Re: [Freesurfer] cannot allocate memory issue

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cannot allocate memory issue It looks like there is too huge a topology error for it to continue: CORRECTING DEFECT 23 (vertices=143258, convex hull=19937) Excessive topologic defect encountered: could not allocate -729782272 edges for retessellation

Re: [Freesurfer] cannot allocate memory issue

From: Allison Stevens Player [astev...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 1:02 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cannot allocate memory issue It looks like there is too huge a topology error

Re: [Freesurfer] cannot allocate memory issue

1:28 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] cannot allocate memory issue You can do: tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix When you downloaded FreeSurfer, you would have also received the subject bert who is a good example

Re: [Freesurfer] cannot allocate memory issue

: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cannot allocate memory issue It says that it couldn't open rh.orig.nofix and lh.orig.nofix. On the popup image, it doesn't look like the skull is present, but it does look like the cerebellum

Re: [Freesurfer] cannot allocate memory issue

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Borzello, Mia Sent: Monday, May 14, 2012 1:37 PM To: Allison Stevens Player Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cannot allocate memory issue It says that it couldn't open rh.orig.nofix and lh.orig.nofix

Re: [Freesurfer] cannot allocate memory issue

: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] cannot allocate memory issue You can do: tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix When you downloaded FreeSurfer, you would have also received the subject bert who is a good example to compare to. He will likely

Re: [Freesurfer] cannot allocate memory issue

...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 3:16 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] cannot allocate memory issue Hi Mia, You may want to check your talairach to make sure that looks okay. If that's not causing the problem, you can edit the wm.mgz to remove

Re: [Freesurfer] cannot allocate memory issue

To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] cannot allocate memory issue You can do: tkmedit subjid filled.mgz rh.orig.nofix -aux-surface lh.orig.nofix When you downloaded FreeSurfer, you would have also received the subject bert who is a good example to compare

Re: [Freesurfer] cannot allocate memory issue

14, 2012 3:16 PM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] cannot allocate memory issue Hi Mia, You may want to check your talairach to make sure that looks okay. If that's not causing the problem, you can edit the wm.mgz to remove the cerebellum

Re: [Freesurfer] cannot allocate memory issue

, 2012 3:32 PM To: Borzello, Mia Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cannot allocate memory issue Hi Mia can you clarify what you mean by a different set of dicoms? Did you acquire more than 1 T1-weighted structural on this subject? And can

Re: [Freesurfer] cannot allocate memory issue

so that's most likely the problem? From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 3:46 PM To: Borzello, Mia Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] cannot allocate memory issue

Re: [Freesurfer] cannot allocate memory issue

: Monday, May 14, 2012 3:32 PM To: Borzello, Mia Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cannot allocate memory issue Hi Mia can you clarify what you mean by a different set of dicoms? Did you acquire more than 1 T1-weighted structural on this subject

Re: [Freesurfer] cannot allocate memory issue

: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 3:46 PM To: Borzello, Mia Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] cannot allocate memory issue actually I wanted one from tkmedit. Can you tell us something about the acquisition

Re: [Freesurfer] cannot allocate memory issue

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, May 14, 2012 3:46 PM To: Borzello, Mia Cc: Allison Stevens Player; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] cannot allocate memory issue actually I wanted one from tkmedit. Can you tell us something about

[Freesurfer] Cannot allocate memory

Hello All, I get the following error while running mri_glmfit. I am using freesurfer V5.0. But qdce seem to run well with the similar settings. -log--- [pthiyyagura@ fsgd]$ mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd --C group.diff.mtx gdfReadHeader: reading

Re: [Freesurfer] Cannot allocate memory

How was fsgd_input.mgh created? What do you get when you run: mri_info fsgd_input.mgh On 10/14/10 7:53 PM, Pradeep wrote: Hello All, I get the following error while running mri_glmfit. I am using freesurfer V5.0. But qdce seem to run well with the similar settings. -log---

RES: [Freesurfer] Cannot allocate memory / can't allocate region

Check ulimit -m That's the max mem per process. ulimit -m 0 Maybe will help. -- Pedro Paulo Jr E71 Nokia -Msg original- De: Jürgen Hänggi Enviada: 01/07/2009 02:36:36 Para: Freesurfer Mailinglist Assunto: [Freesurfer] Cannot allocate memory / can't allocate region Dear FS experts

Re: [Freesurfer] Cannot allocate memory / can't allocate region

Hi Juergen, how much ram do you have in the machine? Bruce On Wed, 1 Jul 2009, Jürgen Hänggi wrote: Dear FS experts I am using high resolution (0.75x0.75x0.75 mm) data within FS but the following error occurred: ... vertex spacing 0.69 +- 0.21 (0.00--6.06) (max @ vno 265258 -- 114262)

[Freesurfer] Cannot allocate memory / can't allocate region

Dear FS experts I am using high resolution (0.75x0.75x0.75 mm) data within FS but the following error occurred: ... vertex spacing 0.69 +- 0.21 (0.00--6.06) (max @ vno 265258 -- 114262) face area 0.19 +- 0.10 (0.00--4.49) mris_make_surfaces(49536) malloc: *** mmap(size=1355776) failed (error

[Freesurfer] Cannot allocate memory

Dear FS experts I tried to make an average subject of 52 subjects, but it seems that an already fixed error is back: Checking 47 /usr/local/freesurfer/subjects/average/tmp/make_average_vol-tmp-12294/seg-Po laris_Male_48.mgh Checking 48

Re: [Freesurfer] Cannot allocate memory

Juergen, Are you running v4.2.0 of linux centos 32b, or asking if this problem was fixed in that version? ie., which version are you running now? I'm not aware of this problem currently (that is, I too thought it was fixed some time ago). Nick On Fri, 2009-02-13 at 16:22 +0100,

Re: [Freesurfer] cannot allocate memory problem when using make average subject

I've put the files back in that location (make_average_*). Run make_average_subject with --no-aseg. But I'm not sure this is the problem. It looks like it is failing when creating the average surface (the fix above is for the volume only). But give it a try. Also, remember to send the entire

[Freesurfer] cannot allocate memory problem when using make average subject

Hi, I was trying to build an average subject using 250 subjects and I got the following error message: processing subject nor76 (246 of 250) reading spherical surface /DATA_FREESURFER/Data/nor76/surf/rh.sphere.reg... reading colortable from annotation file... colortable with 35 entries read