Hi Pablo,
maybe your file is not clean and contains strange symbols to separate
coumns and rows?
Make sure columns are all separated by spaces.
You could load the table into exel or openoffice spreadsheet and then
export as CSV with space (or you could also try tab) for the separation
and no "" around values.
Best, Martin
On 10/19/2015 11:32 AM, pablo najt wrote:
Dear Martin and FS experts.
I am having difficulty in loading my qdec.table.dat to Matlab.
When I use the [command:/Qdec = fReadQdec('qdec.table.dat');/ ] Matlab
only recognises a matrix of 140x1 cell, whereas instead it should
recognise a 140x4.
I tried to import the table as 'table' from the gui interface but then
I am getting error on the command: /M = Qdec2num(Qdec,1)/
Any tips on how to load my table would be fabulous help.
Thank you
Pablo
------------------------------------------------------------------------
To: freesurfer@nmr.mgh.harvard.edu
From: mreu...@nmr.mgh.harvard.edu
Date: Mon, 19 Oct 2015 09:04:41 -0400
Subject: Re: [Freesurfer] Volumes differ in acquisition paramaters
Hi Kasper,
if you use the same file formats and conversion tools across both time
points, the images should be identical. Even after conversion to nii.
Not sure why they are not.
Yes, both warnings are related to the acquisition parameters. The
second should better say that header information is different or
something like that. I see if I can improve that error message to be
more specific in a future release.
Best, Martin
On 10/17/2015 08:59 AM, Kasper Jessen wrote:
Hi Bruce,
Thank you for your reply.
Initially a PAR/REC file was used to obtain an anat.nii file. This
is used to create the [CROSS]. Two timepoints ([CROSS-1] and
[CROSS-2]) was used to create the [BASE].
* Is it because there is too many file formats, and if so, how
should this be managed? Is it possible to run freesurfer
directly from the PAR/REC file?
* Is the “Image geometries differ across time” related to the
difference in acquisition parameters mentioned in the warning?
Best regards
Kasper Jessen
2015-10-10 16:12 GMT+02:00 Bruce Fischl
<fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>:
Hi Kasper
what was your input volume? The .02sec change in TR won't mean
anything,
although it is a bit surprising to see, as is the fact that
the other
parameters (flip angle, TE, etc...) don't seem to be
preserved. We usually
read those right out of the dicom files if that is what you
used as input.
Not sure why we would preserve the TR but not the other
parameters.
cheers
Bruce
On Sat, 10 Oct 2015, Kasper Jessen wrote:
>
> Dear Freesurfer group,
>
> When looking through the log after running recon-all, i have
noticed two
> different errors in the logs. The one being about 'volumes
differ in
> acquisition parameters' and the other 'Image geometries
differ across time,
> maybe due to aquisition changes?'.
>
> Volumes differ in acquisition parameters
> v1acq fa=0.000000 tr=10.032000 te=0.000000 ti=0.000000
> v2acq fa=0.000000 tr=10.012000 te=0.000000 ti=0.000000
> WARNING: Image geometries differ across time, maybe due to
aquisition
> changes?
> This can potentially bias a longitudinal study! Will
continue in 10s.
>
> What do the above errors mean and is it something we should
be worried
> about?
>
> Best regards,
> Kasper Jessen
> MD, PhD Student
>
>
>
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Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
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_______________________________________________ Freesurfer mailing
list Freesurfer@nmr.mgh.harvard.edu
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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.
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Freesurfer@nmr.mgh.harvard.edu
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
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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
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