this only has to do with the qcache part of recon-all, so you could use version 5.3 recon-all -qcache and it should be fine. However, it is not a good idea to try to publish using the analysis from the version of FS that you used. That was a beta version of version 6 and things will change.
On 03/15/2016 01:56 PM, Kaiming Yin wrote:
Dear Douglas,
Is there anything I can do now to fix this now? I don't want to re-run all the data again.
Thanks,
Kaiming
On 15 March 2016 at 16:53, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:
OK, this is a bug that I found and fixed in early Nov. Sorry,
that's part of the danger of using a beta version.
On 03/14/2016 12:22 PM, Kaiming Yin wrote:
Dear Douglas,
I re-run the "-qcache" on one data and it took 8 mins to
finish. Still the files are the same, all in 668.6kB size.
Kaiming
On 14 March 2016 at 15:56, Douglas Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
I don't know what happened. I cannot replicate it here.
Can you
re-run the recon-all -s -qcache command and verify that
the files
are still the same?
On 3/14/16 11:11 AM, Kaiming Yin wrote:
Dear Douglas,
Yes, both of the two pairs of files are the same. i.e.
mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh
diffcount 0
mri_diff rh.thickness.fwhm10.fsaverage.mgh
rh.area.fwhm10.fsaverage.mgh
diffcount 0
Does this mean I run the "-qcache" wrongly? I just run
"recon-all
-s XX -qcache" on each subject.
Thanks,
Kaiming
On 14 March 2016 at 14:58, Douglas Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>> wrote:
Check whether rh.ad_hv.thick.10.mgh and
rh.ad_hv.area.10.mgh
are the same, ie,
mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh
If those are the same, then check whether
thickness.fwhm10.fsaverage and
area.fwhm10.fsaverage are the
same in each subject
On 3/14/16 10:53 AM, Kaiming Yin wrote:
Dear Douglas,
My command lines were, e.g. right thickness
and right white
surface (using the same ad_hv.fsgd and
group_diff.mtx files
in the command lines):
ad_hv.fsgd
GroupDescriptorFile 1
Title AD_HV_GroupAnalysis
Class AD
Class HV
InputAD_003AD
InputAD_005AD
...
InputHV_ABHV
InputHV_AEHV
group_diff.mtx
1 -1
right thickness
mris_preproc --fsgd ad_hv.fsgd --cache-in
thickness.fwhm10.fsaverage --target fsaverage
--hemi rh
--out rh.ad_hv.thick.10.mgh
mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd
ad_hv.fsgd dods
--C group_diff.mtx --surf fsaverage rh
--cortex --glmdir
rh.ad_hv.thick.glmdir
mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir
--cache 4 neg
--cwp 0.05 --2spaces
right white surface
mris_preproc --fsgd ad_hv.fsgd --cache-in
area.fwhm10.fsaverage --target fsaverage
--hemi rh --out
rh.ad_hv.area.10.mgh
mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd
ad_hv.fsgd dods
--C group_diff.mtx --surf fsaverage rh
--cortex --glmdir
rh.ad_hv.area.glmdir
mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir
--cache 4 neg
--cwp 0.05 --2spaces
Their results were all the same.
Thanks,
Kaiming
---------- Forwarded message ----------
From: Douglas N Greve
<greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu>>>
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc:
Date: Mon, 7 Mar 2016 18:47:11 -0500
Subject: Re: [Freesurfer] group analysis all
measures same
results
what are your command lines?
On 5 March 2016 at 02:01, Kaiming Yin
<yinkaiming6987@gmail.com
<mailto:yinkaiming6987@gmail.com>
<mailto:yinkaiming6987@gmail.comgreve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:yinkaiming6987@gmail.com>>>
wrote:
Dear guys,
I was doing group analysis (command-line)
on two groups
(patients and control, no age or other
information). The
data has been "qcached", and after
following the three
steps as "mris_preproc, mri_glmfit and
mri_glmfit-sim"
shown in the tutorial on the Freesurfer
website, I
obtained the difference on thickness in
both left and
right hemispheres, which seems great.
However, when I
repeated the above steps on other
measures, e.g. area,
area.pial, volume (also replaced the parts of
"thickness" in the command lines), the
results seemed to
be exactly the same again as those in the
thickness
comparison, even the p-value numbers in
the file
"cache.th40.neg.sig.cluster.summary" were
the same. I
was using Freesurfer v6.0-beta, and I
performed the
individual data analysis on a linux
cluster and I
copied/downloaded the whole "qcached"
subject directory
to my linux laptop to perform the group
comparison, both
using the same version of Freesurfer, does
it matter? Or
do you know why it happened like this?
Thanks,
Kaiming
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
Phone Number: 617-724-2358 <tel:617-724-2358>
Fax: 617-726-7422 <tel:617-726-7422>
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Outgoing:
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--
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/