Yes that is done that way. I thought you wanted to rerun the cross sectional data from scratch. But you can use your existing setup and run base and long on top of it. But avoid mixing freesurfer versions if posdible.

Best martin

Sent via the Samsung Galaxy S™ III, an AT&T 4G LTE smartphone

-------- Original message -------- From: Jonathan Holt whatsdac@umich.edu Date: To: Martin Reuter mreuter@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: importing from nifti

would it be possible to use volumes generated from recon-all -s <subjID> into the second and third steps of the longitudinal processing workflow?

On Tue, Jul 2, 2013 at 2:24 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: In the meantime you can check how the mri/orig/001.mgz and the mri/orig.mgz and mri/orig_nu.mgz look.

Best, Martin

On 07/02/2013 02:16 PM, Jonathan Holt wrote: Thanks Martin,

I have attached recon-all.log. I tried to run the process several times, I clearly forgot to pass -all that time but I know for certain the first time I tried I passed -all and it provided the same issue. I can pass the dicom images but I'll have to wait for my PI to return in lab.

On Tue, Jul 2, 2013 at 2:05 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: Hi Jonathan,

I changed the subject of the thread, to better reflect this problem, it (so far) has nothing to do with longitudinal processing.

Next time, can you send the log file,  it is in  /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/scripts/recon-all.log not the output on the screen.

But first lets check these:

- your command in the email below seems to be missing "-all"? Probably you passed it?

- and from your screen output it looks like there is a problem importing the nifit:

WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume...

So you need to check the orientation of your  /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/mri/orig/001.mgz...

Not sure why your nifti files are incomplete. Can you point -i to the original dicom?

Best, Martin

On 07/02/2013 01:13 PM, Jonathan Holt wrote: and the command

nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii

On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt whatsdac@umich.edu wrote: Here ya go (to list)

On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt whatsdac@umich.edu wrote: Here ya go.

On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote: No, it's not nifti, that should work.

Can you send me your log file and the command you issued.

Thanks, Martin

On 07/01/2013 03:13 PM, Jonathan Holt wrote: Martin,

definitely passing my images and naming time points appropriately. I have been passing nifti as opposed to dicom and it's entirely possible that may be the issue?

jon On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:

Hi Jon,

are you passing your images? <tpNid> is a placeholder for the id of your subject+time point, for example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path to the dicom files, point it to the first file in the MPRAGE series (or multi echo mprage or what you are using). This is the full path on your file system to that file.

Best, Martin

On 07/01/2013 02:29 PM, Jonathan Holt wrote: I have tried to inspect the tal xfms that were created in the brief time this string was running

recon-all -all -s <tpNid> -i path_to_tpN_dcm

while viewing orig.mgz in tkmedit. they were talairach.xfm and talairach.auto.xfm, both were empty and the tkmedit window was empty.

upon further inspection the log file is complaining about my nifty.

WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information

On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: can you cc the list so that others can answer?

On Mon, 1 Jul 2013, Jonathan Holt wrote:

I have not and I am not certain how to do so

On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote:

Hi Jon

have you visually inspected the results of the tal xform? Bruce On Mon, 1 Jul 2013, Jonathan Holt wrote:

Log file indicates manual talairach alignment may be necessary. ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary Can anyone provide direction. Alternatively, the error indicates talairach alignment can be skipped with -notal-check flag. Is this step completely necessary? jon

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