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.mgzmghRead(/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 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 To: pvaltti@hotmail.com; 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 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.

_______________________________________________ Freesurfer mailing list 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.

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 13ASubject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjectsActual FREESURFER_HOME /home/esther/Freesurfer/freesurferLinux 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.dcmdcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient13ARef Series No = 7Found 23 files, checking for dicomsFound 21 dicom files in series.First SortingComputing Slice DirectionVs: -0.598129 1.13977 6.88063Vs: -0.0854471 0.162824 0.982948Second SortingCounting framesnframes = 1nslices = 21ndcmfiles = 21PE Dir = ROW (dicom read)TransferSyntaxUID: --1.2.840.10008.1.2.1--Loading pixel dataTR=500.00, TE=9.00, TI=0.00, flip angle=90.00i_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 2013done------------------------------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

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/

OK. Thanks ! ;)

Date: Fri, 8 Mar 2013 13:16:10 -0500 From: greve@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: nicks@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Time

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

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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

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...

> > Current Stamp:

freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0

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> > INFO: SUBJECTS_DIR is

/home/esther/Freesurfer/freesurfer/subjects

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...

> > 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

...

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> > > > mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13B > >

/home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz

...

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> > corRead(): can't open file > >

/home/esther/Freesurfer/freesurfer/subjects/Patient13B/COR-.info

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...

> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter

Exp $

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...

> > 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/

-- 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

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.mgzmri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0001.dcm out.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $reading from /home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0001.dcm...Starting DICOMRead2()dcmfile = /home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007--2095579184-0001.dcmdcmdir = /home/esther/Freesurfer/freesurfer/subjects/Patient3BRef Series No = 9Found 22 files, checking for dicomsFound 20 dicom files in series.First SortingComputing Slice DirectionVs: 0.260945 -0.596504 6.96965Vs: 0.0372779 -0.0852149 0.995665Second SortingCounting framesnframes = 1nslices = 20ndcmfiles = 20PE Dir = ROW (dicom read)TransferSyntaxUID: --1.2.840.10008.1.2.1--Loading pixel dataTR=466.66, TE=9.00, TI=0.00, flip angle=90.00i_ras = (-0.9993, -0, -0.0374158)j_ras = (-0.00317395, -0.996363, 0.0851462)k_ras = (-0.0372779, 0.0852149, 0.995665)writing to out.mgz...mghWrite(out.mgz, -1): could not open fileERROR: failure writing out.mgz[esther@IP132-207-67-224 /]$ ------------------ 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

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

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 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/

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...

...

>

---

Freesurfer mailing list 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.

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

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095579184-0

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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

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...

001.dcm... Starting DICOMRead2() dcmfile=/home/esther/Freesurfer/freesurfer/subjects/Patient3B/IM-0007-

-2095579184-

...

0

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...

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

...

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...

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> [ 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

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-s

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...

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>> 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

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>>> Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.

0

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>>> INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjec

ts

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>>> 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

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>>> 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-

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...

0001.dcm

...

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> >>> /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mg

z

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>>> >>> mri_convert >>> >/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--209

545777

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6-

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0001.dcm

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> >>> /home/esther/Freesurfer/freesurfer/subjects/13A/mri/orig/001.mg

z

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>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp

$

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>>> reading from >>> >/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--209

545777

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6-

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0001.dcm...

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>>> Starting DICOMRead2() >>> dcmfile = >>> >/home/esther/Freesurfer/freesurfer/subjects/Patient13A/IM-0006--209

545777

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6-

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...

0001.dcm

...

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>>> 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

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2013

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...

>>> 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?

...

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...

...

>>>> 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

...

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...

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>>>>> 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 >>>>> >>>>> >>> >

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--

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>>>>> 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

...

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>>>>> 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

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...

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>>>>> 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

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>>>>> 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

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...

...

...

...

>>>>> 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

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...

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...

> 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

_______________________________________________ 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.

_______________________________________________ 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.