looks like you don't have permission to write to that directory (or the disk is full)
On Fri, 8 Mar 2013, Valtina Pouegue wrote:
VP,I try FreeView,, tit<s really nice! I dont really know what going on, i try mri-convert with another subject aand i get this:
[esther@IP132-207-67-224 /]$ mri_convert $SUBJECTS_DIR/Patient3B/IM-0007--2095579184-0001.dcm out.mgz mri_convert/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0 001.dcm out.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0 001.dcm... Starting DICOMRead2() dcmfile =/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0 001.dcm dcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient3B Ref Series No = 9 Found 22 files, checking for dicoms Found 20 dicom files in series. First Sorting Computing Slice Direction Vs: 0.260945 -0.596504 6.96965 Vs: 0.0372779 -0.0852149 0.995665 Second Sorting Counting frames nframes = 1 nslices = 20 ndcmfiles = 20 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=466.66, TE=9.00, TI=0.00, flip angle=90.00 i_ras = (-0.9993, -0, -0.0374158) j_ras = (-0.00317395, -0.996363, 0.0851462) k_ras = (-0.0372779, 0.0852149, 0.995665) writing to out.mgz... mghWrite(out.mgz, -1): could not open file ERROR: failure writing out.mgz [esther@IP132-207-67-224 /]$
I thiought that the software automatically created the out.mgz....
Date: Fri, 8 Mar 2013 13:39:51 -0500 From: fischl@nmr.mgh.harvard.edu To: greve@nmr.mgh.harvard.edu CC: pvaltti@hotmail.com; freesurfer@nmr.mgh.harvard.edu;
nicks@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Time
or even
freeview -v /path/to/dicomfile On Fri, 8 Mar 2013, Douglas N Greve wrote:
No, you can just run tkmedit -f subject/mri/orig/001.mgz You do not need to run recon-all to get a volume, you can just run mri_convert, eg mri_convert /path/to/dicomfile out.mgz tkmedit -f out.mgz
doug
On 03/08/2013 12:54 PM, Valtina Pouegue wrote:
If i'm right, the command: > recon-all -s 13A -all execute the whole segmentation ( between 20-40 hours). So , if I just want the see the volume, I have to to the segmentation [ absolutely] ? VP
Date: Fri, 8 Mar 2013 12:36:34 -0500 From: greve@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; nicks@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Time
You will need to run the full processing stream. You can do that from the beginning with
recon-all -i $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s 13A -all
but now that you have a file there, you can run
recon-all -s 13A -all
doug
On 03/08/2013 12:31 PM, Valtina Pouegue wrote:
I convert my set of DICOM of the folder 'Patient13A'
[esther@IP132-207-67-224 ~]$ recon-all -i $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.dcm -s 13A Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjects Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 22:54:16 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux /home/esther/Freesurfer/freesurfer/subjects/13A
mri_convert
/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-
0001.dcm
/home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz
mri_convert
/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-
0001.dcm
/home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from
/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-
0001.dcm...
Starting DICOMRead2() dcmfile =
/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--2095457776-
0001.dcm
dcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient13A Ref Series No = 7 Found 23 files, checking for dicoms Found 21 dicom files in series. First Sorting Computing Slice Direction Vs: -0.598129 1.13977 6.88063 Vs: -0.0854471 0.162824 0.982948 Second Sorting Counting frames nframes = 1 nslices = 21 ndcmfiles = 21 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=500.00, TE=9.00, TI=0.00, flip angle=90.00 i_ras = (-0.992199, 0.0759614, 0.0988506) j_ras = (-0.0907614, -0.983726, -0.155063) k_ras = (0.0854471, -0.162824, 0.982948) writing to /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz...
#------------------------------------------
recon-all -s 13A finished without error at Fri Mar 8 11:37:30 EST
2013
done
After i executed the tkmedit.......... VP > Date: Fri, 8 Mar 2013 12:26:14 -0500 > From: greve@nmr.mgh.harvard.edu > To: pvaltti@hotmail.com > CC: freesurfer@nmr.mgh.harvard.edu; nicks@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Time > > Does that file exist? What was your command to create the mgz file? > On 03/08/2013 12:12 PM, Valtina Pouegue wrote: >> Hi, >> I convert my files and i get news folders with one file with the >> extension .mgz in the folder orig. But , when i try to loasd the >> volume, I get an error >> ------------- >> [esther@IP132-207-67-224 ~]$ tkmedit 13A orig.mgz >>
mghRead(/home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig.mgz,
>> -1): could not open file >> >> >> Error: Loading volume orig.mgz >> >> Couldn't read the anatomical volume. >> >> Tkmedit couldn't read the volume you specified. >> This could be because the image format wasn't recognized, >> or it couldn't find the proper header, >> or the file(s) were unreadable, >> or it was the wrong size. >> ------------------- >> >> could you please help me ? >> >> VP >> >>
>> From: nicks@nmr.mgh.harvard.edu >> Date: Thu, 7 Mar 2013 21:11:31 -0500 >> To: pvaltti@hotmail.com >> CC: freesurfer@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Time >> >> yes, if you give it the filename of the first .dcm in the
series, the
>> software will find the other slices and create the .mgz. >> >> >> >> On Mar 7, 2013, at 9:02 PM, Valtina Pouegue <pvaltti@hotmail.com >> mailto:pvaltti@hotmail.com> wrote: >> >> Oh yes. It's my mistake. But should I give the adress of the first >> file of my set for having the result in .mgz. >> Thanks. >> >> >>> Date: Thu, 7 Mar 2013 16:00:53 -0500 >>> From: greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu
>>> To: pvaltti@hotmail.com mailto:pvaltti@hotmail.com; >> Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Time >>> >>> You cannot give recon-all a folder as input. It must be an image >> file. >>> If you have multiple files, you need multiple -i flags. >>> doug >>> >>> >>> On 03/07/2013 03:48 PM, Valtina Pouegue wrote: >>>> Hi, >>>> Here it is >>>> [esther@IP132-207-67-224 ~]$ recon-all -i >>>> /home/esther/Freesurfer/freesurfer/subjects/Patient13B -s 13B >>>> Subject Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
>>>> Current Stamp:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
>>>> INFO: SUBJECTS_DIR is
/home/esther/Freesurfer/freesurfer/subjects
>>>> Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer >>>> Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 >> 22:54:16 >>>> UTC 2012 x86_64 x86_64 x86_64 GNU/Linux >>>> /home/esther/Freesurfer/freesurfer/subjects/13B >>>> >>>> mri_convert >> /home/esther/Freesurfer/freesurfer/subjects/Patient13B >>>>
/home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz
>>>> >>>> mri_convert >> /home/esther/Freesurfer/freesurfer/subjects/Patient13B >>>>
/home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz
>>>> corRead(): can't open file >>>>
/home/esther/Freesurfer/freesurfer/subjects/Patient13B/COR-.info
>>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
Exp $
>>>> reading from >> /home/esther/Freesurfer/freesurfer/subjects/Patient13B... >>>> >>>> VP >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu mailto: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 >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >> mailto: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 it is >>> addressed. If you believe this e-mail was sent to you in error >> and the e-mail >>> contains patient information, please contact the Partners >> Compliance HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent >> to you in error >>> but does not contain patient information, please contact the >> sender and properly >>> dispose of the e-mail. >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ 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 it
>> is addressed. If you believe this e-mail was sent to you in
error and
>> the e-mail contains patient information, please contact the
Partners
>> Compliance HelpLine at http://www.partners.org/complianceline
. If
the >> e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of
the
e-mail. > > -- > 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 > Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > _______________________________________________ > 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 Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer