On 22 February 2010 15:48, Justin Ales
<justin.ales@gmail.com> wrote:
I think you're missing the leading / in your full path
home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/
should be:
/home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/
and the export line should be:
export SUBJECTS_DIR=~/Desktop/Allimages/MRIscan/
SUBJECTS_DIR is the directory which contains ALL subjects _not_ the
current subject.
Justin Ales
From: Sita Kakunoori <sita@nmr.mgh.harvard.edu>
To: Janani Dhinakaran <janinthesky@gmail.com>
Date: Mon, 22 Feb 2010 10:26:50 -0500 (EST)
Subject: Re: [Freesurfer] recon-all doesn't recon-all
Hi Jan,
Please try rerunning recon-all after removing the spaces or special
characters (if there are any) in the dicom files.
Sita.
On Mon, 22 Feb 2010, Janani Dhinakaran wrote:
Is this what you meant:
First I tried
s0964091@CRIC-0012:~$ recon-all
home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
ERROR: Flag
home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
unrecognized.
home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC
2010 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Feb 22 14:39:27 GMT 2010
Then I tried putting full path in front of both file sets
s0964091@CRIC-0012:~$ recon-all -i
home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm
-i
home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm
-s subj001
ERROR: cannot find
home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm
Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC
2010 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Feb 22 14:41:36 GMT 2010
Jan
On Mon, Feb 22, 2010 at 7:36 AM,
<freesurfer-request@nmr.mgh.harvard.edu> wrote:
> Send Freesurfer mailing list submissions to
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>
> Today's Topics:
>
> 1. recon-all doesn't recon-all (Janani Dhinakaran)
> 2. Re: recon-all doesn't recon-all (Janani Dhinakaran)
> 3. Difference between aparc+aseg and aparc.a2009s+aseg
> (Mohammed el Morabit)
> 4. Re: recon-all doesn't recon-all (Sita Kakunoori)
> 5. Re: mri_vol2surf resulting in different dimensions for two
> different images in the same space (Joonkoo Park)
>
>
> ---------- Forwarded message ----------
> From: Janani Dhinakaran <janinthesky@gmail.com>
> To: freesurfer@nmr.mgh.harvard.edu
> Date: Mon, 22 Feb 2010 11:36:48 +0000
> Subject: [Freesurfer] recon-all doesn't recon-all
> Hello,
> I ran recon-all on Friday. It ran for around a minute instead of 30-48 hours. Unfortunately, when I try tkmedit and other such commands, the pictures don't visualise.
> So today I first confirmed that the SUBJECTS_DIR was in Desktop path. (Because over the weekend it had gone back to usr/local... path and so I re-exported it just now.)
> Then I tried running recon-all again.
>
>
> s0964091@CRIC-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ echo $SUBJECTS_DIR
> Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
> s0964091@CRIC-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001
> ERROR: SUBJECTS_DIR Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does not exist.
>
> Can anyone help me understand what I can do?
> Thanks
> Jan
> --
> I am the Sun, I know no darkness.
>
>
> ---------- Forwarded message ----------
> From: Janani Dhinakaran <janinthesky@gmail.com>
> To: "Xue, Feng" <xfgavin@gmail.com>, freesurfer@nmr.mgh.harvard.edu
> Date: Mon, 22 Feb 2010 14:44:58 +0000
> Subject: Re: [Freesurfer] recon-all doesn't recon-all
> Is this what you meant:
>
> First I tried
> s0964091@CRIC-0012:~$ recon-all home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
> ERROR: Flag home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM unrecognized.
> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
> Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC 2010 x86_64 GNU/Linux
>
> recon-all exited with ERRORS at Mon Feb 22 14:39:27 GMT 2010
>
> Then I tried putting full path in front of both file sets
>
>
> s0964091@CRIC-0012:~$ recon-all -i home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm -i home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001
> ERROR: cannot find home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm
> Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC 2010 x86_64 GNU/Linux
>
> recon-all exited with ERRORS at Mon Feb 22 14:41:36 GMT 2010
>
> Jan
>
>
> On 22 February 2010 14:30, Xue, Feng <xfgavin@gmail.com> wrote:
>>
>> Try with full path, e.g.
>> /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
>>
>> On Mon, Feb 22, 2010 at 7:36 PM, Janani Dhinakaran
>> <janinthesky@gmail.com> wrote:
>> > Hello,
>> > I ran recon-all on Friday. It ran for around a minute instead of 30-48
>> > hours. Unfortunately, when I try tkmedit and other such commands, the
>> > pictures don't visualise.
>> > So today I first confirmed that the SUBJECTS_DIR was in Desktop path.
>> > (Because over the weekend it had gone back to usr/local... path and so I
>> > re-exported it just now.)
>> > Then I tried running recon-all again.
>> >
>> >
>> > s0964091@CRIC-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$
>> > echo $SUBJECTS_DIR
>> > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
>> > s0964091@CRIC-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$
>> > recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i
>> > Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001
>> > ERROR: SUBJECTS_DIR
>> > Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does not exist.
>> >
>> > Can anyone help me understand what I can do?
>> > Thanks
>> > Jan
>> > --
>> > I am the Sun, I know no darkness.
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>>
>>
>>
>> --
>> Best Regards
>>
>> Xue, Feng Phd. candidate
>> Major in Developmental Cognitive Neuroscience
>>
>> National Key Laboratory of Cognitive Neuroscience and Learning
>> Beijing Normal University
>> Beijing, China. 100875
>> Tel: +86-13810154455
>> web: http://psychbrain.bnu.edu.cn
>> ==============================================
>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University
>> telnet://bbs.mdjs.org
>> http://bbs.mdjs.org
>
>
>
> --
> I am the Sun, I know no darkness.
>
>
> ---------- Forwarded message ----------
> From: "Mohammed el Morabit" <M.elMorabit@student.TUDelft.NL>
> To: <freesurfer@nmr.mgh.harvard.edu>
> Date: Mon, 22 Feb 2010 16:05:53 +0100
> Subject: [Freesurfer] Difference between aparc+aseg and aparc.a2009s+aseg
>
> Dear all,
>
> I am using freesurfer to generate a parcellation on the cortex. The regions of this demarced cortex serve as ROIs in further research. My question is... what is the difference between aparc+aseg and aparc.a2009s+aseg? And which one should I use?
>
> Thanx in advance
>
> Morabit.
>
> ---------- Forwarded message ----------
> From: Sita Kakunoori <sita@nmr.mgh.harvard.edu>
> To: Janani Dhinakaran <janinthesky@gmail.com>
> Date: Mon, 22 Feb 2010 10:26:50 -0500 (EST)
> Subject: Re: [Freesurfer] recon-all doesn't recon-all
>
> Hi Jan,
>
> Please try rerunning recon-all after removing the spaces or special characters (if there are any) in the dicom files.
>
> Sita.
>
>
>
> On Mon, 22 Feb 2010, Janani Dhinakaran wrote:
>
>> Is this what you meant:
>>
>> First I tried
>> s0964091@CRIC-0012:~$ recon-all
>> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
>> ERROR: Flag
>> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
>> unrecognized.
>> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
>> Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC
>> 2010 x86_64 GNU/Linux
>>
>> recon-all exited with ERRORS at Mon Feb 22 14:39:27 GMT 2010
>>
>> Then I tried putting full path in front of both file sets
>>
>>
>> s0964091@CRIC-0012:~$ recon-all -i
>> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm
>> -i
>> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0004-0001-00001.dcm
>> -s subj001
>> ERROR: cannot find
>> home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/Dhinakaran^Janani^-0002-0001-00001.dcm
>> Linux CRIC-0012 2.6.31-19-generic #56-Ubuntu SMP Thu Jan 28 02:39:34 UTC
>> 2010 x86_64 GNU/Linux
>>
>> recon-all exited with ERRORS at Mon Feb 22 14:41:36 GMT 2010
>>
>> Jan
>>
>>
>> On 22 February 2010 14:30, Xue, Feng <xfgavin@gmail.com> wrote:
>>
>>> Try with full path, e.g.
>>> /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
>>>
>>> On Mon, Feb 22, 2010 at 7:36 PM, Janani Dhinakaran
>>> <janinthesky@gmail.com> wrote:
>>>>
>>>> Hello,
>>>> I ran recon-all on Friday. It ran for around a minute instead of 30-48
>>>> hours. Unfortunately, when I try tkmedit and other such commands, the
>>>> pictures don't visualise.
>>>> So today I first confirmed that the SUBJECTS_DIR was in Desktop path.
>>>> (Because over the weekend it had gone back to usr/local... path and so I
>>>> re-exported it just now.)
>>>> Then I tried running recon-all again.
>>>>
>>>>
>>>> s0964091@CRIC-0012
>>>
>>> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$
>>>>
>>>> echo $SUBJECTS_DIR
>>>> Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM
>>>> s0964091@CRIC-0012
>>>
>>> :~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$
>>>>
>>>> recon-all -i Dhinakaran^Janani^-0002-0001-00001.dcm -i
>>>> Dhinakaran^Janani^-0004-0001-00001.dcm -s subj001
>>>> ERROR: SUBJECTS_DIR
>>>> Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM does not exist.
>>>>
>>>> Can anyone help me understand what I can do?
>>>> Thanks
>>>> Jan
>>>> --
>>>> I am the Sun, I know no darkness.
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>
>>>
>>>
>>> --
>>> Best Regards
>>>
>>> Xue, Feng Phd. candidate
>>> Major in Developmental Cognitive Neuroscience
>>>
>>> National Key Laboratory of Cognitive Neuroscience and Learning
>>> Beijing Normal University
>>> Beijing, China. 100875
>>> Tel: +86-13810154455
>>> web: http://psychbrain.bnu.edu.cn
>>> ==============================================
>>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University
>>> telnet://bbs.mdjs.org
>>> http://bbs.mdjs.org
>>>
>>
>>
>>
>>
>
>
>
> ---------- Forwarded message ----------
> From: Joonkoo Park <joonkoo@umich.edu>
> To: Douglas N Greve <greve@nmr.mgh.harvard.edu>
> Date: Mon, 22 Feb 2010 10:36:51 -0500
> Subject: Re: [Freesurfer] mri_vol2surf resulting in different dimensions for two different images in the same space
> Thanks Doug,
>
> Where can I find the surface annotation for the fsaverage (or any
> other template) data?
> I will need to import the data into matlab eventually, so I'm thinking
> that the surface annotation file should be readable using load_mgh.m
> (and writable using save_mgh.m). I'm very new to FreeSurfer so I'd
> really appreciate if you can describe each step for me.
>
> Thank you.
>
> Joon
>
>
>
> On Fri, Feb 19, 2010 at 11:47 AM, Douglas N Greve
> <greve@nmr.mgh.harvard.edu> wrote:
>> You're better off loading in the surface annotation directly rather than
>> dealing with aparc+aseg. To make surf2surf output the right dimensions, add
>> --noreshape.
>>
>> doug
>>
>> Joonkoo Park wrote:
>>>
>>> Dear Surfers,
>>>
>>> I (successfully) resampled a functional data on the surface map using
>>> mri_vol2surf:
>>>
>>>
>>>>
>>>> mri_vol2surf --mov func.nii --reg register.dat --projfrac 0.5 --interp
>>>> nearest --hemi lh --o lh.func.mgh
>>>>
>>>
>>> Then, I normalized this image to a standard space (fsaverage) using
>>> mri_surf2surf:
>>>
>>>
>>>>
>>>> mri_surf2surf --srcsubject sub1 --trgsubject fsaverage --sval
>>>> sub1/lh.func.mgh --tval sub1/lh.func.norm.mgh --fwhm 5 --cortex --hemi lh
>>>>
>>>
>>> The dimension of the output file, lh.func.norm.mgh, was 163842 x 1 x 1
>>> (identified from mri_info). This file can be opened from Matlab, and I
>>> can successfully get access to 163842 vertices. What I want now is to
>>> take the aparc+aseg information from the average brain (fsaverage) and
>>> be able identify which vertex falls under which ROI label. I decided
>>> to resample aparc+aseg.mgz in fsaverage on the surface map, hoping to
>>> get label information at the dimension of 163842 x 1 x 1. So I ran:
>>>
>>>
>>>>
>>>> mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage
>>>> --projfrac 0.5 --interp nearest --hemi lh --o fsaverage/surf/lh.roi.mgh
>>>> mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage
>>>> --projfrac 0.5 --interp nearest --hemi rh --o fsaverage/surf/rh.roi.mgh
>>>>
>>>
>>> The resulting mgh files, however, had a dimension of 23406 x 1 x 7.
>>>
>>> 1. As I said, I wanted to get label information (roi number from the
>>> FreeSurferColorLUT) for each vertex of the surface image in the
>>> fsaverage space. Is this the right approach? And did I do this
>>> correctly (I'm concerned about many options above)?
>>>
>>> 2. If so, why is the resulting dimension different from the other one?
>>> I assume that it's probably a reshape issue, but how I can reshape the
>>> dimension to match 163842 x 1 x 1?
>>>
>>> Thanks in advance.
>>>
>>> Joon
>>>
>>> --
>>> Joonkoo Park
>>> Ph.D. Candidate, Cognition & Cognitive Neuroscience
>>> Department of Psychology, University of Michigan
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> greve@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358 Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>