what are you trying to do? If run a recon, your first command should have a -all at the end of it
cheers Bruce
On Fri, 8 Mar 2013, Valtina Pouegue wrote:
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--2
095579184-0
001.dcm out.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ readingfrom/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--20955791
84-0
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--209545777
6-
0001.dcm
>> /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mgz >> >> mri_convert >> /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--209545777
6-
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--209545777
6-
0001.dcm...
>> Starting DICOMRead2() >> dcmfile = >> /home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--209545777
6-
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