what file do you source to set up the env?

On 01/16/2014 01:12 PM, Tessa Vuper wrote:

I am using version 5- Stable 5 Nightly.

On Jan 16, 2014, at 1:00 PM, Douglas N Greve wrote:

...

What version of FreeSurfer are you using?

On 01/16/2014 12:39 PM, Tessa Vuper wrote:

...

Hi all,

I receive the following error when I run the selxavg3 -sess command:

ERROR: cannot find /usr/local/freesurfer/stable5/bin/fsl.5.0.2.xyztrans.sch

Any thoughts on how to fix this?

Thank you so much for your help, tessa

Tessa Vuper Clinical Research Coordinator, Manoach Lab Psychiatric Neuroimaging, MGH Martinos Center for Biomedical Imaging 617-726-1908

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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: https://gate.nmr.mgh.harvard.edu/filedrop2 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

Hi Tessa, I don't know what nmrenv5 is. Is this one of your programs or your lab's? I would use stable53. The stable nightly is actually fairly unstable since we are updating "stable" for eventual release as a new stable. stable53 will not change.

doug

On 01/17/2014 10:47 AM, Tessa Vuper wrote:

When I open the terminal, I type nmrenv5 --> setenv USE_STABLE_5_NIGHTLY --> nmrenv5 again. Should I be sourcing /usr/local/freesurfer/nmr-stable53-env instead?

On Jan 16, 2014, at 1:14 PM, Douglas N Greve wrote:

...

what file do you source to set up the env?

On 01/16/2014 01:12 PM, Tessa Vuper wrote:

...

I am using version 5- Stable 5 Nightly.

On Jan 16, 2014, at 1:00 PM, Douglas N Greve wrote:

...

What version of FreeSurfer are you using?

On 01/16/2014 12:39 PM, Tessa Vuper wrote:

...

Hi all,

I receive the following error when I run the selxavg3 -sess command:

ERROR: cannot find /usr/local/freesurfer/stable5/bin/fsl.5.0.2.xyztrans.sch

Any thoughts on how to fix this?

Thank you so much for your help, tessa

Tessa Vuper Clinical Research Coordinator, Manoach Lab Psychiatric Neuroimaging, MGH Martinos Center for Biomedical Imaging 617-726-1908

---

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: https://gate.nmr.mgh.harvard.edu/filedrop2 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/