Re: [Freesurfer] Qdec does not change the color bar though the color scare is reversed on the brain.

[Knut J Bjuland]

I sent a wrong link. The correct link is here.

I have gone through the tutorials using qdec and when I reverse the values the 
color bar is not reversed.


With reversed color values age verse thickens

http://tjinfo.uib.no/Vedlegg?id=9720b934c5a5a437924453ddb23497b2

Without reversed color values age verse thickens


http://tjinfo.uib.no/Vedlegg?id=0c18c8445e29c173fcf02a208ca1c255





On 07/25/2011 10:06 PM, Knut J Bjuland wrote:
> HI
>
> I have reproduce the error by using the group data from
> buckner_tutorials. The files may be download
> from this link with the error
> http://vedlegg.uib.no/?id=0c18c8445e29c173fcf02a208ca1c255 and with none
> reversal of values
> http://vedlegg.uib.no/?id=20e06d09dcc450ff4abcd85e1e5ab1c5. Is there a
> error with my installation?
>
>
> Cheers
> Knut J
>
> On 07/25/2011 05:09 PM, Knut J Bjuland wrote:
>> Hi
>>
>> I have a problem when using qdec. When I check the option reverse values
>> there color on the brain switch color, but the color bar stays the same.
>> Is there anything that might be wrongs in my files? Is there anything
>> that I might edit in Qdec configuration file?  I do not know what kind
>> of log that are required and I would be happy to send them.
>>
>> Cheers
>>
>> Knut J Bjuland
>>
>> figure attachment
>>
>> http://vedlegg.uib.no/?id=73435c1da0c1f0c1ba792601c4fa1199
>> http://vedlegg.uib.no/?id=20e06d09dcc450ff4abcd85e1e5ab1c5
>>
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Re: [Freesurfer] WM and ASEG edition... recon-all continue command...

[Gonzalo Rojas Costa]

Hi Bruce:

   Maybe I didn't explain clearly my question... I did a complete 
processing of a patient, then I must edit wm.mgz and aseg.mgz because I 
found some segmentation errors... Which recon-all command must I run to 
reprocess the study to use the edited files (wm.mgz and aseg.mgz) ?...

   Sincerely,


Gonzalo Rojas Costa


El 25-07-2011 18:51, Bruce Fischl escribió:
> -make all should work.
>
> cheers
> Bruce
> On Mon, 25 Jul 2011, Gonzalo Rojas Costa wrote:
>
>> Hi
>>
>> I editted the wm.mgz and aseg.mgz files... Which recon-all command
>> must I use to continue the processing ?...
>>
>> Sincerely,
>>
>>
>> Gonzalo Rojas Costa
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>>
>>
>>
>
>
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> 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
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[Freesurfer] mri_surfcluster coordinates

[Chris Hyatt]

Dear Freesurfers,

I know that Qdec outputs coordinates in a "Freesurfer specific space", rather 
than in Talairach space, per this old thread

https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2008-November/008878.html

However, I found that mri_surfcluster (Freesurfer v5.0) in its summary output 
also outputs coordinates in this same "Freesurfer specific space", even though 
the columns indicate TalX, TalY and TalZ. I was going to use this summary info 
to list the location of the statistical maxima of each cluster in a cortical 
thickness p-map. 

Is this a bug in mri_surfcluster? Any suggestions on how to get the coordinate 
data?

Here is the summary info for the left hemisphere (note the positive TalX 
values, when all X values should be negative):

# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
# $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
# CreationTime 2011/07/23-17:08:39-GMT
# cmdline mri_surfcluster --in ./lh.CvsA.glmdir/group.diff/sig.mgh --subject 
fsaverage --hemi lh --surf inflated --thmin 1.301 --sum 
lh.CvsA.thickness.summary --oannot ./lh.CvsA.thickness.annot 
# cwd /prod4/other/freesurfer/glm_cth/age_of_onset
# sysname  Linux
# hostname everest
# machine  x86_64
# FixVertexAreaFlag 1
# FixSurfClusterArea 1
# 
# Input  ./lh.CvsA.glmdir/group.diff/sig.mgh
# Frame Number  0
# srcsubj fsaverage
# hemi lh
# surface inflated
# SUBJECTS_DIR /prod4/other/freesurfer/subjects
# SearchSpace_mm2 62822.2
# SearchSpace_vtx 163842
# Bonferroni 0
# Minimum Threshold 1.301
# Maximum Threshold infinity
# Threshold Signabs
# AdjustThreshWhenOneTail 1
# Area Threshold0 mm^2
# Overall max 2.53286 at vertex 81529
# Overall min -2.67513 at vertex 24566
# NClusters  36
# Total Cortical Surface Area 62822.2 (mm^2)
# FixMNI = 1
# 
# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZNVtxs
   1   -2.675   24566287.98  7.6   95.90.5   533
   22.533   81529 83.49 -7.4  -28.4   50.2   199
   32.5306795386.88-15.4  -86.6   -9.4   677
   4   -2.496  129236 79.10-27.0   27.1   22.6   166
   5   -2.483  138360227.18 -5.7   84.62.6   343
   62.481   18891211.45  3.4  -96.6  -26.2   373
   72.460   33958277.19 37.65.5   15.4   354


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Re: [Freesurfer] WM and ASEG edition... recon-all continue command...

[Bruce Fischl]

-make all should work.

cheers
Bruce
On Mon, 25 Jul 2011, Gonzalo Rojas Costa wrote:

> Hi
>
>  I editted the wm.mgz and aseg.mgz files... Which recon-all command
> must I use to continue the processing ?...
>
>  Sincerely,
>
>
> Gonzalo Rojas Costa
> ___
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>
>
>
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[Freesurfer] WM and ASEG edition... recon-all continue command...

[Gonzalo Rojas Costa]

Hi

  I editted the wm.mgz and aseg.mgz files... Which recon-all command
must I use to continue the processing ?...

  Sincerely,


Gonzalo Rojas Costa
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[Freesurfer] lesion question

[Rebecca McCourt]

Hello everyone,

I have several patients with large cortical lesions (haemorrhage).  I want
to have subcortical structure volumes reflect the lesion, i.e. show up as
hypointensities in aseg.mgz (which they're not right now). However I also
want to calculate cortical thickness, and the WM & GM surfaces around the
lesion are way off. The lesion is much too big to fill manually in wm.mgz.
Any suggestions?

- Rebecca
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Re: [Freesurfer] Dimension error - mri_segstats

[Jaichander S]

Hi,

For others who are looking for the solution to the problem I mentioned
earlier -

Running mri_vol2surf in step3 of the instructions given here (
http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness),
replacing '--reshape' with '--rf 6' did the trick for me. I tried this after
going throught the help for mri_vol2surf command.

Cheers,
Jaichander


From: Jaichander S 
> Subject: [Freesurfer] Dimension error - mri_segstats
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi freesurfers,
>
> I performed ROI cortical thickness measurements earlier on an older version
> of FS as described on
> http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and I
> was able to get the required values.
>
> Now I have the latest version of FS. I draw an ROI mask using FSL software
> and then use it to follow the instructions on the tutorial. The ROI and the
> initial T1 image are in the same coordinate space (with different
> dimensions) as is required by the procedure. After following all the steps
> I
> get
>
> ERROR: dimension mismatch between input volume and seg
> input 27307 1 6
> seg   23406 1 7
>
> when running mri_segstats.
>
> This has been reported by some other people already on the mailing list but
> the suggestions do not work for me. Any light that you can shed to sidestep
> this dimensions problem will be greatly appreciated.
>
> Is there any other workflow to define a volume ROI and then get the
> cortical
> thickness in the area.
>
> Thanks!
> Jaichander
> ------ next part --
> An HTML attachment was scrubbed...
> URL:
> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110725/b2ca0802/attachment-0001.html
>
>
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Re: [Freesurfer] ROI analysis with label in both hemispheres -still looking for an answer

[Katie Bettencourt]

Are there instructions for how to do volume functional analysis and how to
do it that way?  I've only ever done surface based analysis.

Katie

On Mon, Jul 25, 2011 at 3:58 PM, Bruce Fischl wrote:

> Hi Katie,
>
> you could do it in the volume, but I doubt there's any way to do it on the
> surface.
>
> cheers
> Bruce
>
> On Mon, 25 Jul 2011, Katie Bettencourt wrote:
>
>  I'm still looking for an answer on this.  If the answer is you can't do
>> it, I'm ok with that, I just would like to know!  Thanks!
>>
>>  Hi all,
>> I was wondering if anyone had any idea if it was possible to combine
>> together ROIs from the separate hemispheres into one ROI (for
>> example LH V1 and RH V1) and then perform a functional ROI analysis on it.
>>  I know how to combine ROIs (through labels_union) and how to
>> do a functional ROI analysis (using func2roi-sess and roisummary-sess),
>> but I don't know if it is possible to do it with a label that
>> runs across both hemispheres.  Thoughts?
>>
>> Thanks,
>> Katie
>>
>>
>>
>>
>>
>
> 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.
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Re: [Freesurfer] Qdec does not change the color bar though the color scare is reversed on the brain.

[Knut J Bjuland]

HI

I have reproduce the error by using the group data from
buckner_tutorials. The files may be download
from this link with the error
http://vedlegg.uib.no/?id=0c18c8445e29c173fcf02a208ca1c255 and with none
reversal of values
http://vedlegg.uib.no/?id=20e06d09dcc450ff4abcd85e1e5ab1c5. Is there a
error with my installation?


Cheers
Knut J

On 07/25/2011 05:09 PM, Knut J Bjuland wrote:
> Hi
>
> I have a problem when using qdec. When I check the option reverse values
> there color on the brain switch color, but the color bar stays the same.
> Is there anything that might be wrongs in my files? Is there anything
> that I might edit in Qdec configuration file?  I do not know what kind
> of log that are required and I would be happy to send them.
>
> Cheers
>
> Knut J Bjuland
>
> figure attachment
>
> http://vedlegg.uib.no/?id=73435c1da0c1f0c1ba792601c4fa1199
> http://vedlegg.uib.no/?id=20e06d09dcc450ff4abcd85e1e5ab1c5
>
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>
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> 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 
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> but does not contain patient information, please contact the sender and 
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>
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[Freesurfer] Dimension error - mri_segstats

[Jaichander S]

Hi freesurfers,

I performed ROI cortical thickness measurements earlier on an older version
of FS as described on
http://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and I
was able to get the required values.

Now I have the latest version of FS. I draw an ROI mask using FSL software
and then use it to follow the instructions on the tutorial. The ROI and the
initial T1 image are in the same coordinate space (with different
dimensions) as is required by the procedure. After following all the steps I
get

ERROR: dimension mismatch between input volume and seg
input 27307 1 6
seg   23406 1 7

when running mri_segstats.

This has been reported by some other people already on the mailing list but
the suggestions do not work for me. Any light that you can shed to sidestep
this dimensions problem will be greatly appreciated.

Is there any other workflow to define a volume ROI and then get the cortical
thickness in the area.

Thanks!
Jaichander
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Re: [Freesurfer] ROI analysis with label in both hemispheres -still looking for an answer

[Bruce Fischl]

Hi Katie,

you could do it in the volume, but I doubt there's any way to do it on 
the surface.


cheers
Bruce
On Mon, 25 Jul 2011, Katie Bettencourt wrote:


I'm still looking for an answer on this.  If the answer is you can't do it, I'm 
ok with that, I just would like to know!  Thanks!

  Hi all,
I was wondering if anyone had any idea if it was possible to combine together 
ROIs from the separate hemispheres into one ROI (for
example LH V1 and RH V1) and then perform a functional ROI analysis on it.  I 
know how to combine ROIs (through labels_union) and how to
do a functional ROI analysis (using func2roi-sess and roisummary-sess), but I 
don't know if it is possible to do it with a label that
runs across both hemispheres.  Thoughts?

Thanks,
Katie



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[Freesurfer] ROI analysis with label in both hemispheres -still looking for an answer

[Katie Bettencourt]

I'm still looking for an answer on this.  If the answer is you can't do it,
I'm ok with that, I just would like to know!  Thanks!

Hi all,
>
> I was wondering if anyone had any idea if it was possible to combine
> together ROIs from the separate hemispheres into one ROI (for example LH V1
> and RH V1) and then perform a functional ROI analysis on it.  I know how to
> combine ROIs (through labels_union) and how to do a functional ROI analysis
> (using func2roi-sess and roisummary-sess), but I don't know if it is
> possible to do it with a label that runs across both hemispheres.  Thoughts?
>
> Thanks,
> Katie
>
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Re: [Freesurfer] Converting from volume label RAS to Talairach

[Jed Singer]

That almost works; tkmedit is giving talairach coordinates of, for a few 
examples:

14.7 23.9 -22.3
24.8 21.9 -18.8
35.6 20.8 -20.9
54.2 14.1 -17.1
61.1 10.9 -9.6
62.3 6.0 -1.8

Running mri_label2label with fsaverage as the target subject yields a label in 
which those same points have the coordinates:

14.877  25.802  -25.101
25.004  23.475  -20.993
35.985  22.497  -23.559
54.764  15.410  -19.482
61.693  11.670  -10.781
62.952  6.235  -1.732

For comparison purposes, the RAS coordinates in the original label are:

12.000  43.000  5.000
21.000  41.000  9.000
31.000  41.000  7.000
48.000  35.000  11.000
54.000  31.000  19.000
55.000  25.000  27.000

And talairach.xfm is:
1.11050.05820.0623   -0.1394
   -0.07611.03760.1083  -21.5909
   -0.0404   -0.07321.0813  -26.6708

Multiplying those RAS coordinates by the given talairach transformation gives 
coordinates of:

   16.0028   22.6522  -24.8958 
   26.1303   20.3252  -20.7878
   37.1110   19.3473  -23.3543 
   55.8898   12.2610  -19.2767
   62.81848.5205  -10.5760
   64.07783.0855   -1.5270

 
The three sets of values are close, but not the same. The discrepancy is really 
making me uncomfortable; any ideas what's going on?

Thanks so much,
Jed

On Jul 22, 2011, at 5:39 PM, Douglas N Greve wrote:

> 
> You're so close! Use fsaverage as the target subject. The output 
> coordinates will be in MNI305 space.
> doug
> 
> 
> 
> Jed Singer wrote:
>> I'm at my wits' end with what seems like it should be an easy question. I 
>> have a lot of volume labels that have been saved for a lot of brains. I want 
>> the Talairach coordinates corresponding to those points. It seems like 
>> mri_label2label should be able to do this, by putting in 'talairach' as the 
>> target subject, but this returns an error that the subject 'talairach' isn't 
>> found:
>> 
>> mri_label2label --srcsubject m00045 --srclabel label/all.label --trgsubject 
>> talairach --trglabel all_talairach.label --regmethod volume
>> 
>> It seems like I should be able to do it manually by loading the 
>> talairach.xfm generated by recon-all and multiplying that matrix by the RAS 
>> points in the labels; this yields results that are pretty close to those 
>> given in tkmedit, but not that close. Usually within a few, sometimes off by 
>> more.
>> 
>> Probably my inability to do this reflects some misunderstanding or lack of 
>> information, but I've been poring over documentation, forum, and wiki for 
>> hours now and feel like I've hit a wall. Any suggestions?
>> 
>> Thanks so much,
>> Jed
>> ___


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Re: [Freesurfer] QC Montages error

[Louis Nicholas Vinke]

Hi Chindhuri,
I don't think we have access to that path where the scripts are. 
Double-check the path names in your script, it looks like some of the path 
names are relative.  Also, make sure you are running the script from the 
right directory to begin with.
-Louis

On Mon, 25 Jul 2011, Chindhuri Selvadurai wrote:

>
> Hello, I have tried troubleshooting this problem in various ways, but I am
> still not able to figure out the problem.
>
> I probably gave more output than necessary.
>
> Does anyone have any idea?
>
> Thank you!
>
>
>> I am getting an error when using a script that combines these 3 actions:
>>
>> preproc.sh
>> std_map_qc_montages.bash
>> put_tpef.bash
>>
>>
>> Freesurfer version 4
>> SUBJECTS_DIR: /cluster/manoach/AS/RespMon12C/subjects
>> Script:
>> /cluster/manoach/AS/RespMon12C/scripts/preproc_std_qc_montages_put_tpef.sh
>>
>> It looks like the preproc-sess finishes okay, but the problem starts
>> afterwards, but I'm not sure how to fix this easily.. it looks like it's
>> looking for files that aren't there, but I haven't gotten this error
>> before.
>>
>> Thanks!
>>
>> Output, with error at end:
>>
>> - mkbrainmask Done -
>>
>> Thu Jul  7 17:15:21 EDT 2011
>> mkbrainmask-sess done
>> 
>> Started at Thu Jul 7 16:54:00 EDT 2011
>> Ended   at Thu Jul  7 17:15:21 EDT 2011
>> preproc-sess done
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No
>> such file or directory
>> cp: cannot stat `./009/lightboxes/tsnr_lightbox.png': No such file or
>> directory
>> cp: cannot stat `./009/lightboxes/tstd_lightbox.png': No such file or
>> directory
>> cp: cannot stat `./009/lightboxes/tmean_lightbox.png': No such file or
>> directory
>> bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No
>> such file or directory
>> cp: cannot stat `./011/lightboxes/tsnr_

Re: [Freesurfer] QC Montages error

[Douglas N Greve]

Hi Chindhuri, I don't know anything about those scripts (I don't think 
that they are distributed with FS). Why are you using version 4?
doug

Chindhuri Selvadurai wrote:
> Hello, I have tried troubleshooting this problem in various ways, but I am
> still not able to figure out the problem.
>
> I probably gave more output than necessary.
>
> Does anyone have any idea?
>
> Thank you!
>
>
>   
>> I am getting an error when using a script that combines these 3 actions:
>>
>> preproc.sh
>> std_map_qc_montages.bash
>> put_tpef.bash
>>
>>
>> Freesurfer version 4
>> SUBJECTS_DIR: /cluster/manoach/AS/RespMon12C/subjects
>> Script:
>> /cluster/manoach/AS/RespMon12C/scripts/preproc_std_qc_montages_put_tpef.sh
>>
>> It looks like the preproc-sess finishes okay, but the problem starts
>> afterwards, but I'm not sure how to fix this easily.. it looks like it's
>> looking for files that aren't there, but I haven't gotten this error
>> before.
>>
>> Thanks!
>>
>> Output, with error at end:
>>
>> - mkbrainmask Done -
>>
>> Thu Jul  7 17:15:21 EDT 2011
>> mkbrainmask-sess done
>> 
>> Started at Thu Jul 7 16:54:00 EDT 2011
>> Ended   at Thu Jul  7 17:15:21 EDT 2011
>> preproc-sess done
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> mri_convert f.nii fskip8.nii --nskip 8
>> nskip = 8
>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
>> reading from f.nii...
>> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-0.76, -0.00683426, -0.00130865)
>> j_ras = (0.0069578, -0.984569, -0.174858)
>> k_ras = (-9.34106e-05, -0.174863, 0.984593)
>> Skipping 8 frames
>> writing to fskip8.nii...
>> bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No
>> such file or directory
>> cp: cannot stat `./009/lightboxes/tsnr_lightbox.png': No such file or
>> directory
>> cp: cannot stat `./009/lightboxes/tstd_lightbox.png': No such file or
>> directory
>> cp: cannot stat `./009/lightboxes/tmean_lightbox.png': No such file or
>> directory
>> bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No
>> such file or directory
>> cp: cannot stat `./011/lightboxes/tsnr_lightbox.png': No such file or
>> directory
>> cp: cannot stat `./011/lightboxes/tstd_lightbox.png': No such file or
>> directory
>> cp: cannot s

[Freesurfer] QC Montages error

[Chindhuri Selvadurai]

Hello, I have tried troubleshooting this problem in various ways, but I am
still not able to figure out the problem.

I probably gave more output than necessary.

Does anyone have any idea?

Thank you!


> I am getting an error when using a script that combines these 3 actions:
>
> preproc.sh
> std_map_qc_montages.bash
> put_tpef.bash
>
>
> Freesurfer version 4
> SUBJECTS_DIR: /cluster/manoach/AS/RespMon12C/subjects
> Script:
> /cluster/manoach/AS/RespMon12C/scripts/preproc_std_qc_montages_put_tpef.sh
>
> It looks like the preproc-sess finishes okay, but the problem starts
> afterwards, but I'm not sure how to fix this easily.. it looks like it's
> looking for files that aren't there, but I haven't gotten this error
> before.
>
> Thanks!
>
> Output, with error at end:
>
> - mkbrainmask Done -
>
> Thu Jul  7 17:15:21 EDT 2011
> mkbrainmask-sess done
> 
> Started at Thu Jul 7 16:54:00 EDT 2011
> Ended   at Thu Jul  7 17:15:21 EDT 2011
> preproc-sess done
> mri_convert f.nii fskip8.nii --nskip 8
> nskip = 8
> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
> reading from f.nii...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.76, -0.00683426, -0.00130865)
> j_ras = (0.0069578, -0.984569, -0.174858)
> k_ras = (-9.34106e-05, -0.174863, 0.984593)
> Skipping 8 frames
> writing to fskip8.nii...
> mri_convert f.nii fskip8.nii --nskip 8
> nskip = 8
> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
> reading from f.nii...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.76, -0.00683426, -0.00130865)
> j_ras = (0.0069578, -0.984569, -0.174858)
> k_ras = (-9.34106e-05, -0.174863, 0.984593)
> Skipping 8 frames
> writing to fskip8.nii...
> mri_convert f.nii fskip8.nii --nskip 8
> nskip = 8
> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
> reading from f.nii...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.76, -0.00683426, -0.00130865)
> j_ras = (0.0069578, -0.984569, -0.174858)
> k_ras = (-9.34106e-05, -0.174863, 0.984593)
> Skipping 8 frames
> writing to fskip8.nii...
> mri_convert f.nii fskip8.nii --nskip 8
> nskip = 8
> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
> reading from f.nii...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.76, -0.00683426, -0.00130865)
> j_ras = (0.0069578, -0.984569, -0.174858)
> k_ras = (-9.34106e-05, -0.174863, 0.984593)
> Skipping 8 frames
> writing to fskip8.nii...
> mri_convert f.nii fskip8.nii --nskip 8
> nskip = 8
> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
> reading from f.nii...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.76, -0.00683426, -0.00130865)
> j_ras = (0.0069578, -0.984569, -0.174858)
> k_ras = (-9.34106e-05, -0.174863, 0.984593)
> Skipping 8 frames
> writing to fskip8.nii...
> mri_convert f.nii fskip8.nii --nskip 8
> nskip = 8
> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
> reading from f.nii...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.76, -0.00683426, -0.00130865)
> j_ras = (0.0069578, -0.984569, -0.174858)
> k_ras = (-9.34106e-05, -0.174863, 0.984593)
> Skipping 8 frames
> writing to fskip8.nii...
> mri_convert f.nii fskip8.nii --nskip 8
> nskip = 8
> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
> reading from f.nii...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.76, -0.00683426, -0.00130865)
> j_ras = (0.0069578, -0.984569, -0.174858)
> k_ras = (-9.34106e-05, -0.174863, 0.984593)
> Skipping 8 frames
> writing to fskip8.nii...
> mri_convert f.nii fskip8.nii --nskip 8
> nskip = 8
> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $
> reading from f.nii...
> TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-0.76, -0.00683426, -0.00130865)
> j_ras = (0.0069578, -0.984569, -0.174858)
> k_ras = (-9.34106e-05, -0.174863, 0.984593)
> Skipping 8 frames
> writing to fskip8.nii...
> bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No
> such file or directory
> cp: cannot stat `./009/lightboxes/tsnr_lightbox.png': No such file or
> directory
> cp: cannot stat `./009/lightboxes/tstd_lightbox.png': No such file or
> directory
> cp: cannot stat `./009/lightboxes/tmean_lightbox.png': No such file or
> directory
> bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No
> such file or directory
> cp: cannot stat `./011/lightboxes/tsnr_lightbox.png': No such file or
> directory
> cp: cannot stat `./011/lightboxes/tstd_lightbox.png': No such file or
> directory
> cp: cannot stat `./011/lightboxes/tmean_lightbox.png': No such file or
> directory
> bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No
> such file or directory
> cp: cannot stat `./013/lightboxes/tsnr_lightbox.png': No such file or
> directory
> cp: cannot stat `./013/lightboxes/tstd_lightbox.png': No s

Re: [Freesurfer] Pial Edits on Base Template

[Martin Reuter]

Hi,

yes, rerunning with force in this case is correct.

If you made edits to cross and want to rerun base, I would recommend to
delete the base first and recreate it from scratch. Any edits in the
base will not be meaningful anyway as the images (and maybe even the
space) will change underneath.

Best, Martin


On Thu, 2011-07-21 at 07:19 -0400, Khoa Nguyen wrote:
> Hi Jeff,
> 
> I think you'll have to run with -force. In the newer version 5.1, this is 
> updated so that you don't have to anymore. And you might be right 
> that deleting the folder is not a good idea since the edits were made in 
> there. If you made edits in the cross and want to rerun the base, then you 
> can either do -force or delete the folder or delete whichever file you 
> made edits on (if made edits on wm.mgz in cross, delete wm.mgz in base).
> 
> Martin, is that correct?
> 
> -Khoa
> 
> On Wed, 20 Jul 2011, Jeff Sadino wrote:
> 
> > Hello,
> >
> > I have a subject with three timepoints I am putting through the longitudinal
> > stream in fs 5.0.0.  After the base template was created, I edited some of
> > the pial surfaces on the base.  Now when I run the command:
> > "recon-all -base subject -autorecon2-pial -autorecon3", it says:
> > "ERROR: /mnt/fs5/050079 exists, delete or re-run with -force"
> > This is confusing to me because if I delete the folder, then wont my edits
> > also be deleted?  I ran it using the force flag, and it seems to be going
> > ok.  I just want to ask if this is the best way to do this.
> >
> > Thank you,
> > Jeff Sadino
> >
> 
> 

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[Freesurfer] Qdec does not change the color bar though the color scare is reversed on the brain.

[Knut J Bjuland]

Hi

I have a problem when using qdec. When I check the option reverse values
there color on the brain switch color, but the color bar stays the same.
Is there anything that might be wrongs in my files? Is there anything
that I might edit in Qdec configuration file?  I do not know what kind
of log that are required and I would be happy to send them.

Cheers

Knut J Bjuland

figure attachment

http://vedlegg.uib.no/?id=73435c1da0c1f0c1ba792601c4fa1199
http://vedlegg.uib.no/?id=20e06d09dcc450ff4abcd85e1e5ab1c5

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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Problems with segmentation

[Bruce Fischl]

Hi Leo

if the pial surface is in the right place in those regions you don't have 
to worry about it.

cheers
Bruce
On Mon, 25 Jul 2011, leonardo kay wrote:

> Hi freesurfers
> 
> After checking recon-all -autorecon-all processing, I realized that a part of 
> the duramadre has been not fully removed (please see attached file).
> Can anyone help me how to solve this please.
> 
> Best regards.
> 
> --
> Leo Kay.
> 
> 
>
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Error in qdec longitudinal 5.1

[Martin Reuter]

Hi Natalia,

check your qdec/.QDECRC file, it needs to contain:

MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc

probably you put a .spc instead of -spc

Best, Martin

On Fri, 2011-07-22 at 18:51 +0200, Natalia h wrote:
> Dear list,
> 
> I got an error after following the newer version of the longitudinal
> stream 5.1.
> 
> long_mris_slopes worked without problems for my data which was
> longtudinally processed in 4.5.
> 
> I also split the qdec.table to the cross for being able to be loaded
> in qdec GUI.
> 
> Somehow I got the error that the
> Templatesubxx/surf/xh.thickness.fwhm.xx.fsaverage.mgh.
> 
> I went back to check inside the Templatesubxx/surf has only the
> xh.long.thickness-xxx.fwhmx.fsaverage.mgh
> 
> Is there something I am missing?
> 
> Thanks a lot for the help
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> 

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Re: [Freesurfer] long_mris_slopes error

[Martin Reuter]

Hi Derin,

there is a know and fixed bug in mris_calc in the 5.1 release. It has
difficulties with very long file names and returns a non zero exit code,
which stops my script in some situations.

I'll ask Nick if he can put up a fixed version of mris_calc for
download.

Best, Martin

On Thu, 2011-07-21 at 15:18 -0500, Derin Cobia wrote:
> I received the follow error while running a set of subjects under
> 'long_mris_slopes,' and wasn't able to decipher the problem.  It
> appears that mris_calc is not able to do the division for these files
> (dividing by 0 perhaps?).  Any help appreciated, here's the command
> and tail end of output/error, thanks.
> 
> 
> -Derin
> 
> 
> > long_mris_slopes --qdec ./qdec/CH_prog.qdec.table.dat --meas
> > thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack
> > --do-label --time scan_interval --qcache fsaverage
> > 
> > 
> > 
> > 
> > ===
> > SUBJECT CH1840 fwhm 0  computing SPC
> > 
> > 
> > mris_calc
> > -o 
> > /disk/NIACAL_01/Trio/NMorph/PROCESSED_DATA/FREESURFER-v5.1.0/CH1840/surf/lh.long.thickness-spc.fwhm0.mgh
> >  ./tmp-CH1840_lh_thickness_FFrRIR/beta1.mgh div 
> > ./tmp-CH1840_lh_thickness_FFrRIR/beta0.mgh
> > 
> > 
> > ERROR 1 : mris_calc compute sym. pct. change (spc) problem?
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[Freesurfer] Problems with segmentation

[leonardo kay]

Hi freesurfers

After checking recon-all -autorecon-all processing, I realized that a part
of the duramadre has been not fully removed (please see attached file).
Can anyone help me how to solve this please.

Best regards.

-- 
Leo Kay.
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Re: [Freesurfer] longitudinal version

[Martin Reuter]

Hi Natalia,

the images in 5.0 are not in the same voxel space across time. Probably
that is what's causing your problems. In 5.1 they are all resampled and
processed in the subjects' template space. So you cannot simply open
stuff on top of each other with 5.0 data. 
However, surfaces are in vertex correspondence even in 5.0 and therefore
I expect long_mris_slopes to work on 5.0 data. long_stats_slopes should
also work with 5.0 data as the stats files should not have changed too
much, but who knows.

Best, Martin

On Thu, 2011-07-21 at 18:40 +0200, Natalia h wrote:
> Hi Martin,
> 
> Thanks for the reply. I updated to 5.1 and loaded the -base and -long
> processed data.
> The -base for two timepoints look fine, but the
> Time1sub1.long.Templatesub1 & Time2sub1.long.Templatesub1 are not well
> aligned.  (p.s  screen shot in the attachment)
> I checked both the pial and white surfaces, as well as the norm volume
> between time points.
> It seems like they are not well registered. I used the mri_convert
> from DICOM to mgz.
> Is there a way to solve this?
> 
> Thank you
> 
> 
> On Mon, Jul 18, 2011 at 9:03 PM, Martin Reuter
>  wrote:
> > Hi Natalia,
> > I have never tried it, but don't see a reason why it should not work. Just 
> > try it out.
> >
> > Best Martin
> >
> > On Jul 18, 2011, at 5:13 AM, Natalia h  wrote:
> >
> >> Dear list,
> >>
> >> I have a question about the longitudinal stream´s version.
> >> I used Freesurfer 4.5 and followed the longitudinal tutorials (the
> >> tutorials "before" June 2011) for my data.
> >> I saw on the updated version, there are scripts which can do the
> >> post-process longitudinal data, like long_mris_slopes,
> >> long_stats_slopes, long_qdec_table.
> >> Can I use these scripts to do the stats even though I used version 4.5
> >> for the longitudinal process?
> >>
> >> Thanks for the help
> >>
> >>
> >
> >
> > 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
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> > error
> > but does not contain patient information, please contact the sender and 
> > properly
> > dispose of the e-mail.
> >

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Re: [Freesurfer] Longitudinal Analysis Error

[Martin Reuter]

Hi Silvia,

qdec does not support any longitudinal analysis (only cross sectional).
So I assume you either compare groups cross sectionally (e.g. at
baseline) or you constructed your own longitudinal measure (e.g. percent
change, within each subject) and then do a cross sectional analysis of
that statistic?
Both these things should work. I think your qdec table is setup
incorrectly?

Best, Martin

On Tue, 2011-07-19 at 12:45 +0200, Silvia Juanes wrote:
> Dear all,
> We are preprocessed our data to perform a longitudinal study using
> longitudinal pipeline of Freesurfer 4.5. However, when we try to do
> the group-analysis using qdec (Freesurfer 5.1), we obtain the
> following error: 
> 
> 
> ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
> ninputs = 64
> Checking inputs
> nframestot = 64
> Allocing output
> Done allocing
> nframes = 64
> Writing to /home/barbara/subjects/qdec/Untitled/y.mgh
> gdfReadHeader: reading /home/barbara/subjects/qdec/Untitled/qdec.fsgd
> INFO: gd2mtx_method is dods
> Reading source surface /home/barbara/subjects/fsaverage/surf/lh.white
> ERROR: no contrasts specified.
> Error in Analyze: command failed: mri_glmfit
> --y /home/barbara/subjects/qdec/Untitled/y.mgh
> --fsgd /home/barbara/subjects/qdec/Untitled/qdec.fsgd dods
> --glmdir /home/barbara/subjects/qdec/Untitled --surf fsaverage lh
> 
> 
> 
> Has anyone experienced a similar problem and is there any way to correct it?
> 
> 
> Best,
> 
> 
> 
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Re: [Freesurfer] Mri_concat: initial frame ok but noisy in output image

[Agnieszka Burzynska]

Hi, 
Thank you for your help! I think there might be something wrong just with
the display, as in fact more brains looked strange. I have re-run the
concatenation with the same commands after killing many processes on my
computer and now all brains look correct and in the expected order.

Cheers,
Aga


On 7/19/11 10:19 PM, "Douglas N Greve"  wrote:

> 
> 
> Hi Aga, that does sound strange. mri_concat does no processing at all,
> so if that subject looks ok before you run mri_concat, it should look
> fine afterwards. Try running just that subject through mri_concat (so
> there's no real concatenation). Also, make sure that the bad subject in
> the mri_concat output is the same subject that you are looking at
> individually; you could be off by 1.
> 
> doug
> 
> Agnieszka Burzynska wrote:
>> 
>> Dear experts,
>> I used mri_concat to concatenate sig.mgh files from fixed-level
>> analysis (combining runs within each subject). All input files when
>> viewed as initial single frame images look correct. For one person,
>> however, in the multiframe image the sig.mgh looks just like noise
>> (see attached picture). I used only --i and --o in the mri_concat
>> command line. What could have happened? I get no error messages and
>> everything else looks ok.
>> 
>> Thank you for your help,
>> Aga
>> 
>> 
>> 
>> 
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[Freesurfer] Atlas coordinates provided by QDEC

[Maria Serra]

Hi FreeSurfer experts,

I have a doubt regarding the atlas coordinates that uses QDEC. In the power
point titulated "fscoordinates" found in the FreeSurferWiki seems that  the
coordinates used are aligned with Talairach Atlas, but when you enter de
coordinates provided by QDEC in a particular area (Right isthmus for
example: -32 -29 26) in a Talairach client software (
http://www.talairach.org/client.html) , the area that it gives you is
totally different:

Label at (-32, -29, 26)
Left Cerebrum, Frontal Lobe, Sub-Gyral, White Matter, *

Do you know why this discrepancy is caused for?

Thank you in advance,


-- 
Maria Serra

PIC (Port d'Informació Científica)
Campus UAB, Edifici D
E-08193 Bellaterra, Barcelona
Telf. +34 93 586 8232
www.pic.es
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[Freesurfer] Problems with the .Qdecrc file

[dolphinede]

 

 Hi,


i am trying to add new measures (pial_lgi) to qdec. I created the .Qdecrc file 
in my SUBJECTS_DIR/qdec, with the described text (MEASURE1 = pial_lgi), but it 
does not work, i cannot select in the qdec menu pial_lgi as a dependent 
variable. A qdec.fsgd file is also in the same place.
I also renamed the .Qderc file in qdec.Qdecrc but it is the same. I am using 
freesurfer version 4.5.0. I am a little bit confused what i can do?


Thanks you a lot,

Best regards 

Daniel


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