I don't think the disk is a problem: I have a lot of space. But in resume, here is exactly what i did ( in order):- I created a folder where I saved the dicoms of my subject- I tried the command
recon-all -i <path-to-first-structural> [-i <path-to-second-structural>] -s <subjid>
like recon-all -i $SUBJECTS_DIR/PatientXX/blablabla.dcm -s XX . - I got a folder with empty folders excepts orig which got a folder name '001.mgz'.- I thought that the file was .mgz was my dicom in .mgz, so I try opened them with tkmedit , and It didn't work- I also launch just after the recon-all command for segmentation .- Just after I try the mri_convert for my subject like ' mri_convert $SUBJECTS_DIR/PatientXX/blablabla.dcm out.mgz- I got an mgz folder in the /mri/- I opened it with tkmedit and I could see the volume So, I retry with another subject , an I got the error described in the previous mail. Did I make a mistake somewhere? VP Date: Fri, 8 Mar 2013 14:19:29 -0500
From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: greve@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; nicks@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Time
looks like you don't have permission to write to that directory (or the disk is full)
On Fri, 8 Mar 2013, Valtina Pouegue wrote:
VP,I try FreeView,, tit<s really nice! I dont really know what going on, i try mri-convert with another subject aand i get this:
[esther@IP132-207-67-224 /]$ 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