Hi Martin,
Thanks!
However, while running the long_MRIS_slopes command, I was met with
following error:
===============================================================================
SUBJECT template_D208AB Stacking Within-Subject Maps
mri_concat JT_D208A_3D_A.long.template_D208AB/surf/lh.thickness
JT_D208B_3D_B.long.template_D208AB/surf/lh.thickness --o
/template_D208AB/surf/lh.long.thickness-stack.mgh
ninputs = 2
Checking inputs
ERROR: dimension mismatch between
JT_D208A_3D_A.long.template_D208AB/surf/lh.thickness and
JT_D208B_3D_B.long.template_D208AB/surf/lh.thickness
ERROR 1 : mri_concat stacking did not work?
I ran mri_inf, with the following output:
Volume information for JT_D208A_3D_A.long.template_D208AB/surf/lh.thickness
type: curv
dimensions: 135222 x 1 x 1
voxel sizes: 1.0000, 1.0000, 1.0000
type: FLOAT (3)
fov: 135222.000
dof: 0
xstart: -67611.0, xend: 67611.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform not present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
0.0000
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a =
0.0000
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s =
0.0000
Orientation : ???
Primary Slice Direction: unknown
voxel to ras transform:
-1.0000 0.0000 0.0000 67611.0000
0.0000 0.0000 1.0000 -0.5000
0.0000 -1.0000 0.0000 0.5000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 0.0000 0.0000 67611.0000
-0.0000 -0.0000 -1.0000 0.5000
-0.0000 1.0000 -0.0000 0.5000
0.0000 0.0000 0.0000 1.0000
Volume information for JT_D208B_3D_B.long.template_D208AB/surf/lh.thickness
type: curv
dimensions: 135130 x 1 x 1
voxel sizes: 1.0000, 1.0000, 1.0000
type: FLOAT (3)
fov: 135130.000
dof: 0
xstart: -67565.0, xend: 67565.0
ystart: -0.5, yend: 0.5
zstart: -0.5, zend: 0.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform not present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
0.0000
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a =
0.0000
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s =
0.0000
Orientation : ???
Primary Slice Direction: unknown
voxel to ras transform:
-1.0000 0.0000 0.0000 67565.0000
0.0000 0.0000 1.0000 -0.5000
0.0000 -1.0000 0.0000 0.5000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 0.0000 0.0000 67565.0000
-0.0000 -0.0000 -1.0000 0.5000
-0.0000 1.0000 -0.0000 0.5000
0.0000 0.0000 0.0000 1.0000
It appears that the dimensions are the same in both images at baseline and
followup. What could I be doing wrongly here? Many thanks!
Best Regards,
Elijah
On Wed, Jun 4, 2014 at 4:58 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu>
wrote:
> The one that comes with Freesurfer. It's always the same.
> Best Martin
>
>
> Sent via my smartphone, please excuse brevity.
>
> -------- Original message --------
> From: Elijah Mak
> Date:06/04/2014 10:54 AM (GMT-05:00)
> To: Martin Reuter
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed
> scans
>
> Hi Martin,
>
> Many thanks for your help!
>
> How is fsaverage created?
>
> I ran all my recon-alls (cross, base, and longs) in a single
> $Subject_DIR folder. Then , I moved the longs and bases to another
> folder for organizational purposes, which explains why the fsaverage
> is missing.
>
> Is the fsverage study-specific? Or can I point the path of the
> fsverage to the same fsaverage that came with the original
> installation of Freesurfer?
>
> Many thanks again.
>
> Best Regards,
> Elijah
>
> On Wed, Jun 4, 2014 at 3:17 PM, Martin Reuter
> <mreu...@nmr.mgh.harvard.edu> wrote:
> > Hi Elijah,
> >
> > Just create a link
> > ln -s pathtofsaverage ./
> >
> > Usually this is done during recon-all
> >
> >
> > Sent via my smartphone, please excuse brevity.
> >
> >
> > -------- Original message --------
> > From: Elijah Mak
> > Date:06/04/2014 7:17 AM (GMT-05:00)
> > To: Martin Reuter ,freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed
> > scans
> >
> > Hi Martin,
> >
> > We corresponded about the longitudinal pipeline earlier. Your help has
> > been much appreciated. I am now at the stage where I am ready to
> > perform QDEC analyses using the 2-stage method.
> >
> > In my Subject DIR, I have all the longs (Tp1 and 2) and their
> > corresponding bases. However, when i run the following command
> >
> > long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness
> > --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label
> > --time years --qcache fsaverage --sd $SUBJECTS_DIR
> >
> >
> > It says that fsaverage is missing.
> >
> > Can I simply copy the fsverage folder from the default Freesurfer
> > "subjects" folder?
> >
> > Many thanks!
> > Best Regards,
> > Elijah
> >
> > On Wed, Jan 15, 2014 at 10:15 PM, Martin Reuter
> > <mreu...@nmr.mgh.harvard.edu> wrote:
> >> Hi Elijah,
> >>
> >>
> >> On 01/15/2014 04:10 PM, Elijah Mak wrote:
> >>
> >> Hi Martin,
> >>
> >> Thank you for your help.
> >>
> >> By re-processing, do you mean running recon-alls all over again?
> >>
> >>
> >> Yes. 5.0 is old and it is better to run everything with 5.3 from
> beginning
> >> to end. If you have a lot of data or a lot of edits, you can try running
> >> -base and -long in 5.3 and keep the independent (cross sectional) stuff
> in
> >> 5.0, but I don't recommend mixing versions.
> >>
> >>
> >>
> >> Could you elaborate on the advantage of creating a new subjectsdir and
> >> copying over the orig dirs for each subject?
> >>
> >> This way you keep a backup copy of your old 5.0 processed data (to
> lookup
> >> edits etc). If you have a script that calls recon-all with the -i flag
> for
> >> inputs, you don't need to copy the mri/orig dirs (it will grab the data
> >> from
> >> the dicoms again). Copying the orig dirs and dropping -i will skip that
> >> step.
> >>
> >>
> >> On a related note, would it be better to run the full recon-all pipeline
> >> for
> >> each subject? I have been running batches of subjects at each stage
> (i.e.
> >> autorecon1, autorecon2, and finally autorecon3).
> >>
> >> Yes, full pipeline (-all) on all subjects is what I usually do. You can
> >> run
> >> individual steps and check intermediate results if you like, but I
> usually
> >> run everything and check everything at the end.
> >>
> >> Best, Martin
> >>
> >>
> >>
> >> Thank you again.
> >>
> >> Best Wishes,
> >> Elijah
> >>
> >>
> >>
> >>
> >> On Wed, Jan 15, 2014 at 9:02 PM, Martin Reuter
> >> <mreu...@nmr.mgh.harvard.edu>
> >> wrote:
> >>>
> >>> Hi Elijah,
> >>>
> >>> if you have minimal edits, I'd recommend to reprocess the data from
> >>> scratch with 5.3 (that is supposed to be the same as using the -clean
> >>> flag
> >>> when rerunning 5.3 on top of the old 5.0 data). But I'd recommend to
> >>> create
> >>> a new subjectsdir, copy over the subjedid/mri/orig dirs for each
> subject
> >>> and
> >>> rerun from scratch with 5.3 the independent, base and long runs.
> >>>
> >>> Best, Martin
> >>>
> >>>
> >>>
> >>> On 01/13/2014 06:18 PM, Elijah Mak wrote:
> >>>
> >>> Greetings Freesurfer Community,
> >>>
> >>> I am running a longitudinal study using Freesurfer v.5.3 to compare
> rate
> >>> of cortical thinning between 2 groups of subjects. I hope I can seek
> some
> >>> expert advice on the following situation:
> >>>
> >>> All data (both the baseline and follow-up) has been processed
> >>> independently using recon-all. This has been done on Freesurfer 5.0.
> >>>
> >>> Since then, I have upgraded to Freesurfer v5.3 to utilize the linear
> >>> mixed
> >>> effect capability.
> >>>
> >>> For the construction of base and longs, I understand that it is
> important
> >>> to add -clean flag to my recon-all strings to overwrite brainmask.mgz
> >>> etc.
> >>> When must this be done?
> >>>
> >>> I am still new to Freesurer, and I'd greatly appreciate any advice
> >>> regarding workflow.
> >>>
> >>> Many Thanks,
> >>>
> >>> Elijah
> >>>
> >>>
> >>>
> >>> --
> >>>
> >>> Elijah Mak, B.A.
> >>>
> >>> Doctoral Candidate | Psychiatry
> >>>
> >>> University of Cambridge | Department of Psychiatry
> >>>
> >>> Trinity College, Cambridge, CB2 1TQ
> >>>
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> Freesurfer mailing list
> >>> Freesurfer@nmr.mgh.harvard.edu
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>> --
> >>> Martin Reuter, Ph.D.
> >>> Assistant in Neuroscience - Massachusetts General Hospital
> >>> Instructor in Neurology - Harvard Medical School
> >>> MGH / HMS / MIT
> >>>
> >>> A.A.Martinos Center for Biomedical Imaging
> >>> 149 Thirteenth Street, Suite 2301
> >>> Charlestown, MA 02129
> >>>
> >>> Phone: +1-617-724-5652
> >>> Email:
> >>> mreu...@nmr.mgh.harvard.edu
> >>> reu...@mit.edu
> >>> Web : http://reuter.mit.edu
> >>>
> >>> 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.
> >>
> >>
> >>
> >>
> >> --
> >>
> >> Elijah Mak, B.A.
> >>
> >> Doctoral Candidate | Psychiatry
> >>
> >> University of Cambridge | Department of Psychiatry
> >>
> >> Trinity College, Cambridge, CB2 1TQ
> >>
> >>
> >>
> >> --
> >> Martin Reuter, Ph.D.
> >> Assistant in Neuroscience - Massachusetts General Hospital
> >> Instructor in Neurology - Harvard Medical School
> >> MGH / HMS / MIT
> >>
> >> A.A.Martinos Center for Biomedical Imaging
> >> 149 Thirteenth Street, Suite 2301
> >> Charlestown, MA 02129
> >>
> >> Phone: +1-617-724-5652
> >> Email:
> >> mreu...@nmr.mgh.harvard.edu
> >> reu...@mit.edu
> >> Web : http://reuter.mit.edu
> >
> >
> >
> > --
> > Elijah Mak, Gates Scholar
> >
> > PhD Candidate | Psychiatry
> >
> > University of Cambridge | Department of Psychiatry
> >
> > Trinity College, Cambridge, CB2 1TQ
> >
> >
>
>
>
> --
> Elijah Mak, Gates Scholar
>
> PhD Candidate | Psychiatry
>
> University of Cambridge | Department of Psychiatry
>
> Trinity College, Cambridge, CB2 1TQ
>
>
>
--
Elijah Mak, Gates Scholar
PhD Candidate *|* Psychiatry
University of Cambridge *| *Department of Psychiatry
Trinity College, Cambridge, CB2 1TQ
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