Thanks, it works! VP
Date: Fri, 8 Mar 2013 14:44:24 -0500 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; nicks@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Time
try giving it the dicoms directly as input (instead of converting first) and make sure you have -all on the recon-all command line and see if that works Bruce On Fri, 8 Mar 2013, Valtina Pouegue wrote:
Just a dial error. I use the all at the end. I have 4 subjects and a set of dicom for each subjects. I would like to convert my dicoms files to be able to make a segmentation with Freesurfer ...
Date: Fri, 8 Mar 2013 14:32:20 -0500 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: nicks@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu; greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Time
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 $SUBJECTS_DIR/PatientXX/blablabla.dcm out.mgz
- I got an mgz folder in the /mri/
- I opened it with tkmedit and I could see the volume
So, I retry with another subject , an I got the error described in the previous mail. Did I make a mistake somewhere? VP
Date: Fri, 8 Mar 2013 14:19:29 -0500
From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: greve@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu;
nicks@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Time
looks like you don't have permission to write to that directory (or the disk is full)
On Fri, 8 Mar 2013, Valtina Pouegue wrote:
VP,I try FreeView,, tit<s really nice! I dont really know what going on, i try mri-convert with another subje
ct
aand i get this:
[esther@IP132-207-67-224 /]$ mri_convert $SUBJECTS_DIR/Patient3B/IM-0007--2095579184-0001.dcm out.mgz mri_convert/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-000
7--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-00
07--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 $SUBJECTS_DIR/Patient13A/IM-0006--2095457776-0001.d
cm
-s
>> 13A -all >> >> but now that you have a file there, you can run >> >> recon-all -s 13A -all >> >> doug >> >> >> On 03/08/2013 12:31 PM, Valtina Pouegue wrote: >>> I convert my set of DICOM of the folder 'Patient13A' >>> ------------ >>> [esther@IP132-207-67-224 ~]$ 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/subjec
ts
>>> 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--209
545777
6-
0001.dcm
> >>> /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mg
z
>>> >>> mri_convert >>> >/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--209
545777
6-
0001.dcm
> >>> /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mg
z
>>> $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--209
545777
6-
0001.dcm...
>>> Starting DICOMRead2() >>> dcmfile = >>> >/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--209
545777
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 E
ST
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 1
3B
>>>>>>> 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 1
9
>>>>> 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.ht
ml
>>>>> 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 pers
on
>>>>> to whom it is >>>>>> addressed. If you believe this e-mail was sent to you in err
or
>>>>> 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 o
f
> 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/
>>
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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.