Re: [Freesurfer] unpacking error

Yes, dcmunpack does not take a -seqcfg argument, so specify each run separately And it can take a while. On 02/04/2016 01:42 PM, Ji Won Bang wrote: > Hi. > > When I tried dcmunpack: > dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ > $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UN

Re: [Freesurfer] unpacking error

Thank you! Best, Ji Won > On Feb 4, 2016, at 7:01 PM, Douglas Greve wrote: > > that is not generated when unpacking. It is generated when you run > preproc-sess > > >> On 2/4/16 6:09 PM, Ji Won Bang wrote: >> Hi, again. >> >> I tried dcmunpack: >> dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/d

Re: [Freesurfer] unpacking error

that is not generated when unpacking. It is generated when you run preproc-sess On 2/4/16 6:09 PM, Ji Won Bang wrote: Hi, again. I tried dcmunpack: dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/ -fsfast -run 3 bold nii f.nii It worked. Inside $DATA_DIR/$SUBJECT/bol

Re: [Freesurfer] unpacking error

Hi, again. I tried dcmunpack: dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/ -fsfast -run 3 bold nii f.nii It worked. Inside $DATA_DIR/$SUBJECT/bold/003/, I see only 2 files: f.nii f-infodump.dat On the instruction page ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFu

Re: [Freesurfer] unpacking error

Hi. When I tried dcmunpack: dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK I had error: ERROR: Flag -seqcfg unrecognized. -src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ /home/jbang/Projects/replay/epi//replay01/b

Re: [Freesurfer] unpacking error

Hi Ji Won, can you try dcmunpack? Should take the same arguments On 2/4/16 10:28 AM, Ji Won Bang wrote: Dear. Freesurfer team. Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and v5.3.0. The command line is: unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_

[Freesurfer] unpacking error

Dear. Freesurfer team. Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and v5.3.0. The command line is: unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK And I get the error message: $Id: unpacksdcmdir,v

[Freesurfer] Unpacking error

Freesurfer team, Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and v5.3.0. The command line is: unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK And I get the error message: $Id: unpacksdcmdir,v 1.19.2

Re: [Freesurfer] unpacking error

Can you upload one of the dicom files (does not matter which one)? On 12/05/2014 11:00 AM, Fan, Qiuyun wrote: > > Dear Freesurfer expert, > > I come across an error message when calling 'unpacksdcmdir' to unpack > the data that's been pushed to Bourget. I have no trouble navigate to > the direc

[Freesurfer] unpacking error

Dear Freesurfer expert, I come across an error message when calling 'unpacksdcmdir' to unpack the data that's been pushed to Bourget. I have no trouble navigate to the directory on /cluster/archive and see the files are there, but just could not have the 'unpacksdcmdir' work. Here are the

Re: [Freesurfer] unpacking error

What is the model of the scanner? I think there is an error in there because it can' find the parameters it needs. You can also try something like mri_convert 160 11147SACC000.MR.RESEARCH_NEURO. test.mgh this might print something more informative to the terminal. You can also try mri_probed

Re: [Freesurfer] unpacking error

That doesn't sound good. Does tag 28, 30 mean the voxel size is missing, why would this be? It is a Siemens dicom from a 3T scanner - not sure which model but I can find out. Do you have any idea why I am getting errors for some runs in the scan. info file as such?: 7 t1_mprage_tra_p2_iso_1.0 err

Re: [Freesurfer] unpacking error

hmmm, if it does not have tag 28 30, then something is really wrong. This is a Siemens dicom, right? What scanner? doug On 05/22/2014 06:05 PM, Caroline Lewis wrote: > Thanks Douglas. Now I am running into other errors. I ran the command: > > unpacksdcmdir -src 0008 -targ 0008/mri/orig -fsfast

Re: [Freesurfer] unpacking error

Thanks Douglas. Now I am running into other errors. I ran the command: unpacksdcmdir -src 0008 -targ 0008/mri/orig -fsfast \ ? -run 8 bold nii 001.nii ERROR: reading 0008/11147SACC000.MR.RESEARCH_NEURO.8.1.2014.05.13.14.42.14.530.48877356.dcm tag 28 30 Also, some of the runs in the "scan.info"

Re: [Freesurfer] unpacking error

Remove the \<> On 05/22/2014 03:45 PM, Caroline Lewis wrote: > Hi, > > I am trying to unpack dicom files and convert them to nifti, but am > running into an error. I ran the following command with no issue: > unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir/scan.info >

[Freesurfer] unpacking error

Hi, I am trying to unpack dicom files and convert them to nifti, but am running into an error. I ran the following command with no issue: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir/scan.info however, when I try to run the next command to actually unpack the data: unpacksdc

Re: [Freesurfer] unpacking error

uot; > (file "/usr/local/freesurfer/stable5_1_0/bin/unpacksdcmdir.tcl" line > 1197) > [grover:SJT037] (nmr-stable5.1-env) > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on beh

Re: [Freesurfer] unpacking error

boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, December 11, 2012 5:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] unpacking error Hi Lindsay, you'll have to give us more informat

Re: [Freesurfer] unpacking error

Hi Lindsay, you'll have to give us more information. Tell us what the command line is and the full terminal output. thanks doug On 12/11/2012 05:20 PM, Staples, Lindsay Katharine wrote: > Hi- > > I don't know much about freesurfer other than the very basics. Can anyone > tell me why I would be

[Freesurfer] unpacking error

Hi- I don't know much about freesurfer other than the very basics. Can anyone tell me why I would be getting the following error when I run the second unpacking command? while executing "close $flfid" ("foreach" body line 149) invoked from within "foreach runcfg $unpackcfg { set Run

Re: [Freesurfer] Unpacking Error

What scanner did these come from? That tag is the pixel spacing. If that is not there, then something is really wrong. doug dmill...@bu.edu wrote: > Hello, > > I was hoping someone may know the answer to this. I am using freesurfer > version 5.1. > > Using this command unpacksdcmdir -src DICOMS/

[Freesurfer] Unpacking Error

Hello, I was hoping someone may know the answer to this. I am using freesurfer version 5.1. Using this command unpacksdcmdir -src DICOMS/"$1"_dicom -targ $1 -fsfast -scanonly $1/scan_"$1".txt where scan_name.txt lists the scan names used in the protocol and $1 is the subject's ID. I keep gett

[Freesurfer] unpacking error:: "exited abnormally"

Hello, I'm trying to unpack a diffusion run and getting this error, "child process excited abnormally". Anyone encounter this before? Here are the details: [purkinje:pat08_sess2_dti] (nmr-stable3-env) unpacksdcmdir -src /space/archive/181/siemens/TrioTim-35162-20080921-182835-474000 -targ /clus

[Freesurfer] Unpacking Error

FreeSurfer Folks, My lab is currently running version 4.0.2 on our server, and since the scanner upgrade we have been unable to unpack our data. When I attempt use the unpacksdcmdir script I get the following error. mri_convert DICOM/08020113/combined//89501876 ./T1_MPRAGE_sag/002 --sdcmlist