[Freesurfer] roi mask?

[Marja Caverlé]

Hi all,

So I ran a recon-all -all on one of my subjects, and it completed without
errors (according to the log). Now I would like to get cortical thickness
numbers from this subject, but when I open the tutorial regarding this, it
says it assumes that you already have a roi mask and a T1 in the same
coordinate space as the roi mask.

Did the recon -all -all by any chance create these files? And if not, how
can I?

So basically the question is; what do I have to do after recon -all -all in
order to get cortical thickness numbers in roi's of my subjects?

Thanks in advance.

Marja
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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Hi Anastasia,

Thank you for your answer.
There aren't stats/*.path.mean.txt files and terminal says 'Could not read
/Applications/freesurfer/subjects/cvs_avg35.' I checked
/Application/freesurfer/subjects/cvs_avg35 folder and couldn't find
COR-.info file.
Could you tell me any resolutions, please?

Thanks,
Anri

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-05-21 6:48 GMT+09:00 Anastasia Yendiki :

>
> Hi Anri - The FA values are extracted in the native space of each subject,
> which is why those are the only coordinates that you see. If you want to
> display the results of your analysis on an average path, after running
> trac-all -stat, you can use the stats/*.path.mean.txt files (see also the
> last part of the TRACULA tutorial).
>
> Best,
> a.y
>
>
> On Wed, 18 May 2016, Anri WATANABE wrote:
>
> Dear experts,
>> I use TRACULA to examine a measure (FA) at each voxel in one pathway.
>> pathstats.byvoxel.txt files show coordinates in native space and after
>> converting those the new files don't show any coordinates which are in MNI
>> space.
>> Could you tell me how can I know MNI coordinate values?
>>
>> Thank you!
>>
>>
>> Regards,
>> Anri
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>>
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Re: [Freesurfer] mris_preproc - srcsubjreg

[Makaretz, Sara Johanna]

Hi Doug, still wondering about this - thanks!


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara Johanna 
[smakar...@mgh.harvard.edu]
Sent: Tuesday, May 24, 2016 16:23
To: Freesurfer support list
Subject: [Freesurfer] mris_preproc - srcsubjreg

Hi Doug, I¹m curious why the newer mris_preproc does not use sphere.reg as
the default srcsurfreg when the target is not fsaverage - see below

Thanks for any info! (not urgent)


On 2016-5-24, 11:30, "Z K"  wrote:

>Good question, and I dont know the answer. mris_preproc is Dougs baby so
>I suggest just posting this question to the list with "mris_preproc" in
>the subject, and I bet he will give you the answer.
>
>-Zeke
>
>On 05/23/2016 10:31 PM, Makaretz, Sara Johanna wrote:
>> Hi Zeke,
>>
>> I am running some surface glms where targ is a patient surface. The help
>> says --target TargetSubject (requires ?h.TargetSubject.sphere.reg), and
>> I was getting errors because dev-default mris_preproc wanted
>> mri_surf2surf to have srcsurfreg =
>> $SUBJECTS_DIR/$srcsubject/surf/$h.$TARGSUBJ.sphere.reg
>>
>> But mris_preproc in 5.3 let me do target = patient surface with no extra
>> surf reg files or extra flags to get mri_surf2surf to use srcsurfreg =
>> $SUBJECTS_DIR/$srcsubject/surf/$h.sphere.reg
>>
>> I had been running this with 5.3:
>> mris_preproc\
>>  --target $TARGSUBJ\
>>  --hemi lh\
>>  --meas thickness\
>>  --fsgd file.fsgd\
>>  --out lh.output.mgh
>>
>> And I was about to email freesurfer@nmr but "for fun" tried adding
>> --surfreg sphere.reg which got mris_surf2surf to use the right reg
>> files. So now I'm selfishly trying to figure this out - do you know what
>> prompted the switch from sphere.reg "opt-out" to sphere.reg "opt-in"?
>> Aka why sphere.reg is non-default when the target is non-fsaverage? Did
>> that make sense? I know there must be some reason, so I really want to
>> know a bit more so I can stay sane when old scripts break.
>>
>> Thanks for any info! Sorry to bother you!
>> Sara
>>
>>
>>
>>
>>
>>
>> Outputs from the FS-dev one:
>>
>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>> 
>> Src lh $TARGSUBJ.sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg
>> $TARGSUBJ.sphere.reg --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg
>> sphere.reg --etcetcetc
>> 
>> ERROR can't find $SUBJECTS_DIR/$SRCSUBJ/surf/$TARGSUBJ.sphere.reg
>> because I never made it
>>
>>
>>
>> Outputs from the FS-dev one with fsaverage as the targ subj:
>>
>> $Id: mris_preproc,v 1.76 2015/12/09 20:02:53 zkaufman Exp $
>> 
>> Src lh sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg
>> --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --etcetcetc
>> 
>> mris_preproc finds everything, runs no problem
>>
>>
>>
>> Outputs from the FS-5.3 one:
>>
>> $Id: mris_preproc,v 1.59.2.4 2012/12/06 16:06:52 mreuter Exp $
>> 
>> Src lh sphere.reg
>> Trg lh sphere.reg
>> 
>> mri_surf2surf --srcsubject $SRCSUBJ --srchemi lh --srcsurfreg sphere.reg
>> --trgsubject $TARGSUBJ --trghemi lh --trgsurfreg sphere.reg --etcetcetc
>> 
>> mris_preproc exits with no errors because everything exists
>>
>>
>>
>>


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Re: [Freesurfer] 答复: 答复: 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

[Hao wen]

Thanks very much, right now, I am clear!


De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Douglas N Greve 

Envoyé : jeudi 26 mai 2016 21:14:28
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] 答复: 答复: 答复: 答复: 答复: Cluster-wise correction error with 
mri_glmfit-sim

That depends on what you expect from your data. If you do not have an
apriori hypothesis about the sign of the contrast you are testing, then
use abs (unsigned). Eg, if your hypothesis is Controls have a thicker
cortex than ADs and you set up your contrast to be gamma =
ThicknessControls - ThicknessADs, then you might expect gamma > 0. By
selecting a sign (pos or neg), you get an advantage in the significance.
But the hypothesis MUST be a priori. You should not play with your data
to see what gives you the best result.

On 05/26/2016 03:07 PM, Hao wen wrote:
> Hi, Doug:
> I check out the documentation for this command: 'mri_surfcluster', and I also 
> played with another comparision, with the --cache value with 1.3 and 4, and I 
> get fewer cluster with 1.3, so right now I got the idea for the --cache 
> value, but Im still confused about how do you decide which sign to use? I 
> know the what the values do for the cluster, but what about the sign?
> Merci
> Hao
> 
> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>  代表 Hao wen 
> 
> 发送时间: 2016年5月26日 20:16:18
> 收件人: freesurfer@nmr.mgh.harvard.edu
> 主题: [Freesurfer] 答复:  答复: 答复: 答复: Cluster-wise correction error with 
> mri_glmfit-sim
>
> Hi, Doug:
> I find something, here r my command:
>
> mri_glmfit-sim \
>--glmdir lh.AD_CN_NO_COVARIATE.glmdir \
>--cache 4 pos \
>--cwp  0.05
>
> so I changed the sign, at first, it was 'neg', after correction, i got no 
> cluster, but with 'pos', I got  Ncluster = 9, and with 'abs', I got Ncluster 
> = 8, So i am a little lost, I checked out the explaination for the 
> 'mri_glmfit-sim ', so my question is that what is the differences for the 
> sign, and what are the thresholds for --cache and --cwp seperately? Hope to 
> hear from you soon!
> Merci
> Best
> Hao
> 
> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>  代表 Douglas N Greve 
> 
> 发送时间: 2016年5月26日 19:27:53
> 收件人: freesurfer@nmr.mgh.harvard.edu
> 主题: Re: [Freesurfer] 答复: 答复: 答复: Cluster-wise correction error with 
> mri_glmfit-sim
>
> They use two different methods. SurfStat uses gaussian random fields and
> FS uses monte carlo simulation. How significant is your cluster in FS?
>
> On 05/26/2016 01:17 PM, Hao wen wrote:
>> Hi:
>> Because I make the group analysis with SurfStat, and I get the cluster after 
>> the clusterwise correction, so I think in Freesurfer, we should have the 
>> similiar result:)
>>
>> 
>> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  代表 Douglas N Greve 
>> 
>> 发送时间: 2016年5月26日 18:22:58
>> 收件人: freesurfer@nmr.mgh.harvard.edu
>> 主题: Re: [Freesurfer] 答复: 答复: Cluster-wise correction error with 
>> mri_glmfit-sim
>>
>> why do you think there shold be a cluster?
>>
>> On 05/26/2016 12:21 PM, Hao wen wrote:
>>> Hi,
>>> I tried every value for the --cache and --cwp, as what i understood, the 
>>> --cache is the threshold for the vertex-wise correction and the --cwp is 
>>> the clusterwise correction, and i even tried the 0.99 with the --cwp, which 
>>> should give me all my cluster, but still, I got nothing, I checked the 
>>> 'mri_glmfit-sim', and it seems not so clear for me, do you there where is 
>>> the problem?
>>>
>>> Merci
>>> Hao
>>> 
>>> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  代表 Douglas N Greve 
>>> 
>>> 发送时间: 2016年5月26日 17:54:58
>>> 收件人: freesurfer@nmr.mgh.harvard.edu
>>> 主题: Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim
>>>
>>> It looks like it worked. there is not an error there. It did not find
>>> any voxels above your chosen level of signficance, but that is not an
>>> error per se
>>>
>>> On 05/26/2016 11:19 AM, Hao wen wrote:
 Doug:

 Thank you for your reply, it does not work, also, I think the problem
 is that for me after the clusterwise correction, I got no corrected
 cluster, I am not sure if it the problem that I set the --cache value
 and the --cwp value, but I changed the value, it always return me nothing!

 This is the msg, it said that found 0 value :


 Computing voxel-wise significance
 CSDpvalMaxSigMap(): found 0/163842 above 0
 Adjusting threshold for 1-tailed test.
 If the input is not a -log10(p) volume, re-run with --no-adjust.
 Searching for Clusters ...
 thmin=1.30 (0.998970), thmax=-1.00 (-1), thsignid=-1,
 minarea=0.00
 Found 2 clusters
 Max cluster size 132.153870
 Pruning by CW P-Value 0.001
 Saving thresholded output to
 lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig

[Freesurfer] Segmentation of a 3D IR-deskulled volume

[Aquino Domenico]

Dear Freesurfer team,


I'm trying to segment a brain from a non standard sequence. It is a 3D IR 
sequence that I have previously pre-elaborated and deskulled.

The software is running from a long time and at the moment is correcting 
defects (17/128) but I'm not sure it's working properly.


I have previously sent you the NIFTI_GZ file but, if you prefer, I'll send it 
using FTP.


Could you please help me in detecting some possible issues?


Thanks a lot,


Domenico



___
Eng. Domenico Aquino
Department of Neuroradiology
IRCCS Foundation Neurological Institute "Carlo Besta"
Via Celoria,11-20133 Milano
Phone: +39 02 23942472
Fax +39 02 23942543


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[Freesurfer] Merging Brain Hemispheres

[Saeed Mahdizadeh Bakhshmand]

Hello,

As we know, Freesurfer generates separate surface models and associated
labels for each brain hemisphere, is there any way to merge two hemisphere
and come up with a single cortex surface?

My best,
Saeed

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Re: [Freesurfer] LME MATLAB, X matrix error

[Hanbyul Cho]

Dear Martin Reuter,

Thank you for your clear explanation.

Best wishes,

Han.

On Tue, May 24, 2016 at 12:41 PM, Martin Reuter  wrote:

> Dear Han,
>
> if controls have only 1 time point, you cannot compare/analyse any
> measurement of change across the groups (such as atrophy rates). You can
> only do a cross sectional analysis at baseline.
> For patients you could separately look at atrophy rates (if they differ
> from zero, which should be true for any type of group - so that alone is
> not very exciting).
> Usually there is only one time column with time-from-baseline for example
>
> me1 0 ...
> me2 1.2 ...
> me 3 1.8 ...
> you1 0 ..
> you2 0.9 ...
> he1 0
> she1 0
> she2 1.1
> and so on (this could be in years). There can be differently many rows per
> subject, depending on the number of time points. Single time point
> subjects, can be mixed in and will help to estimate cross subject
> variances, but they won't really help much with estimates of longitudinal
> changes. Having a full group with only a single time point does not make
> sense in a longitudinal design.
>
> Best, Martin
>
>
>
> On 05/21/2016 06:42 PM, Hanbyul Cho wrote:
>
> Dear Martin Reuter,
>
> Thank you for your reply.
>
> Our patients have several time points, but controls have only 1 time
> points,
> so when I coded the patients group =1, controls groups = 0 ,
> the 2. time  and  3. time2 column were same as 5. 4.X time 6. 4.X time2
> column.
> and 8. 7. X time and 9. 8. X time2 were all zeros.
>
> And then, how about this X matrix (Subjects N X 5)?
>
> 1. Intercept (all '1')
> 2. 4.X time (from baseline time point)
> 3. 4.X time2
> 4. age
> 5. extra values for covariate
>
> is it a vallid matrix for test the effects of group X time2 ?
>
>
> Thank you,
>
> Han.
>
> On Sat, May 21, 2016 at 3:13 PM, Martin Reuter <
> mreu...@nmr.mgh.harvard.edu> wrote:
>
>> Hi Han,
>> Try to find a local statistician to help you with your analysis.
>> About your matrix: rows need to be number of all time points from all
>> subject. Time 2 should probably not be there. Also columns 7-9 need to be
>> dropped (they are just the negative of the rows before).
>>
>> Best Martin
>> On May 21, 2016 3:32 PM, Hanbyul Cho  wrote:
>>
>> Dear FreeSurfer Team,
>>
>> I processed in MATLAB for Linear Mixed Effects Models Analysis with this
>> X matrix:
>>
>> X matrix is 'Subjects N X 11', 11 columns are as follow,
>>
>> 1. Intercept (all '1')
>> 2. time (from baseline time point)
>> 3. time2
>> 4. Patients group = 1, Control = 0
>> 5. 4.X time
>> 6. 4.X time2
>> 7. Patients group = 0, Control = 1
>> 8. 7. X time
>> 9. 8. X time2
>> 10. age
>> 11. extra values for covariate
>>
>>
>> 1.
>> When I process this command,
>> [lhTh01,lhRe01] = lme_mass_fit_EMinit(X,[1],Y,ni,lhcortex,3,4)
>> The MATLAB windows print the warning alarm repeatedly.
>> " Warning: Matrix is close to singular or badly scaled. Results may be
>> inaccurate."
>> Is this X matrix something wrong?
>>
>>
>> 2.
>> After complete   'lme_mass_fit_EMinit' process with the warning, I tried
>> the next command,
>> [lhRgs01,lhRgMeans01] = lme_mass_RgGrow(lhsphere, lhRe01,
>> lhTh01,lhcortex,2,95);
>> This command took a long time to process, and it caused the whole stop
>> MATLAB works.
>> Is it also because of the X matrix...?
>>
>>
>> Could you let me know the solution for the X matrix problems ?
>>
>> Best Wishes,
>>
>> Han
>>
>>
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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
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
>
> ___
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> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> --
> 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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>
>
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> 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 

Re: [Freesurfer] 答复: 答复: 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

[Douglas N Greve]

That depends on what you expect from your data. If you do not have an 
apriori hypothesis about the sign of the contrast you are testing, then 
use abs (unsigned). Eg, if your hypothesis is Controls have a thicker 
cortex than ADs and you set up your contrast to be gamma = 
ThicknessControls - ThicknessADs, then you might expect gamma > 0. By 
selecting a sign (pos or neg), you get an advantage in the significance. 
But the hypothesis MUST be a priori. You should not play with your data 
to see what gives you the best result.

On 05/26/2016 03:07 PM, Hao wen wrote:
> Hi, Doug:
> I check out the documentation for this command: 'mri_surfcluster', and I also 
> played with another comparision, with the --cache value with 1.3 and 4, and I 
> get fewer cluster with 1.3, so right now I got the idea for the --cache 
> value, but Im still confused about how do you decide which sign to use? I 
> know the what the values do for the cluster, but what about the sign?
> Merci
> Hao
> 
> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>  代表 Hao wen 
> 
> 发送时间: 2016年5月26日 20:16:18
> 收件人: freesurfer@nmr.mgh.harvard.edu
> 主题: [Freesurfer] 答复:  答复: 答复: 答复: Cluster-wise correction error with 
> mri_glmfit-sim
>
> Hi, Doug:
> I find something, here r my command:
>
> mri_glmfit-sim \
>--glmdir lh.AD_CN_NO_COVARIATE.glmdir \
>--cache 4 pos \
>--cwp  0.05
>
> so I changed the sign, at first, it was 'neg', after correction, i got no 
> cluster, but with 'pos', I got  Ncluster = 9, and with 'abs', I got Ncluster 
> = 8, So i am a little lost, I checked out the explaination for the 
> 'mri_glmfit-sim ', so my question is that what is the differences for the 
> sign, and what are the thresholds for --cache and --cwp seperately? Hope to 
> hear from you soon!
> Merci
> Best
> Hao
> 
> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>  代表 Douglas N Greve 
> 
> 发送时间: 2016年5月26日 19:27:53
> 收件人: freesurfer@nmr.mgh.harvard.edu
> 主题: Re: [Freesurfer] 答复: 答复: 答复: Cluster-wise correction error with 
> mri_glmfit-sim
>
> They use two different methods. SurfStat uses gaussian random fields and
> FS uses monte carlo simulation. How significant is your cluster in FS?
>
> On 05/26/2016 01:17 PM, Hao wen wrote:
>> Hi:
>> Because I make the group analysis with SurfStat, and I get the cluster after 
>> the clusterwise correction, so I think in Freesurfer, we should have the 
>> similiar result:)
>>
>> 
>> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  代表 Douglas N Greve 
>> 
>> 发送时间: 2016年5月26日 18:22:58
>> 收件人: freesurfer@nmr.mgh.harvard.edu
>> 主题: Re: [Freesurfer] 答复: 答复: Cluster-wise correction error with 
>> mri_glmfit-sim
>>
>> why do you think there shold be a cluster?
>>
>> On 05/26/2016 12:21 PM, Hao wen wrote:
>>> Hi,
>>> I tried every value for the --cache and --cwp, as what i understood, the 
>>> --cache is the threshold for the vertex-wise correction and the --cwp is 
>>> the clusterwise correction, and i even tried the 0.99 with the --cwp, which 
>>> should give me all my cluster, but still, I got nothing, I checked the 
>>> 'mri_glmfit-sim', and it seems not so clear for me, do you there where is 
>>> the problem?
>>>
>>> Merci
>>> Hao
>>> 
>>> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  代表 Douglas N Greve 
>>> 
>>> 发送时间: 2016年5月26日 17:54:58
>>> 收件人: freesurfer@nmr.mgh.harvard.edu
>>> 主题: Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim
>>>
>>> It looks like it worked. there is not an error there. It did not find
>>> any voxels above your chosen level of signficance, but that is not an
>>> error per se
>>>
>>> On 05/26/2016 11:19 AM, Hao wen wrote:
 Doug:

 Thank you for your reply, it does not work, also, I think the problem
 is that for me after the clusterwise correction, I got no corrected
 cluster, I am not sure if it the problem that I set the --cache value
 and the --cwp value, but I changed the value, it always return me nothing!

 This is the msg, it said that found 0 value :


 Computing voxel-wise significance
 CSDpvalMaxSigMap(): found 0/163842 above 0
 Adjusting threshold for 1-tailed test.
 If the input is not a -log10(p) volume, re-run with --no-adjust.
 Searching for Clusters ...
 thmin=1.30 (0.998970), thmax=-1.00 (-1), thsignid=-1,
 minarea=0.00
 Found 2 clusters
 Max cluster size 132.153870
 Pruning by CW P-Value 0.001
 Saving thresholded output to
 lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh
 Saving cluster numbers to
 lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh
 Saving cluster pval
 lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh


 Do you have any idea?

 Best

 Hao

 ---

[Freesurfer] 答复: 答复: 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

[Hao wen]

Hi, Doug:
I check out the documentation for this command: 'mri_surfcluster', and I also 
played with another comparision, with the --cache value with 1.3 and 4, and I 
get fewer cluster with 1.3, so right now I got the idea for the --cache value, 
but Im still confused about how do you decide which sign to use? I know the 
what the values do for the cluster, but what about the sign?
Merci
Hao

发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Hao wen 
发送时间: 2016年5月26日 20:16:18
收件人: freesurfer@nmr.mgh.harvard.edu
主题: [Freesurfer] 答复:  答复: 答复: 答复: Cluster-wise correction error with 
mri_glmfit-sim

Hi, Doug:
I find something, here r my command:

mri_glmfit-sim \
  --glmdir lh.AD_CN_NO_COVARIATE.glmdir \
  --cache 4 pos \
  --cwp  0.05

so I changed the sign, at first, it was 'neg', after correction, i got no 
cluster, but with 'pos', I got  Ncluster = 9, and with 'abs', I got Ncluster = 
8, So i am a little lost, I checked out the explaination for the 
'mri_glmfit-sim ', so my question is that what is the differences for the sign, 
and what are the thresholds for --cache and --cwp seperately? Hope to hear from 
you soon!
Merci
Best
Hao

发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Douglas N Greve 

发送时间: 2016年5月26日 19:27:53
收件人: freesurfer@nmr.mgh.harvard.edu
主题: Re: [Freesurfer] 答复: 答复: 答复: Cluster-wise correction error with 
mri_glmfit-sim

They use two different methods. SurfStat uses gaussian random fields and
FS uses monte carlo simulation. How significant is your cluster in FS?

On 05/26/2016 01:17 PM, Hao wen wrote:
> Hi:
> Because I make the group analysis with SurfStat, and I get the cluster after 
> the clusterwise correction, so I think in Freesurfer, we should have the 
> similiar result:)
>
> 
> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>  代表 Douglas N Greve 
> 
> 发送时间: 2016年5月26日 18:22:58
> 收件人: freesurfer@nmr.mgh.harvard.edu
> 主题: Re: [Freesurfer] 答复: 答复: Cluster-wise correction error with mri_glmfit-sim
>
> why do you think there shold be a cluster?
>
> On 05/26/2016 12:21 PM, Hao wen wrote:
>> Hi,
>> I tried every value for the --cache and --cwp, as what i understood, the 
>> --cache is the threshold for the vertex-wise correction and the --cwp is the 
>> clusterwise correction, and i even tried the 0.99 with the --cwp, which 
>> should give me all my cluster, but still, I got nothing, I checked the 
>> 'mri_glmfit-sim', and it seems not so clear for me, do you there where is 
>> the problem?
>>
>> Merci
>> Hao
>> 
>> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  代表 Douglas N Greve 
>> 
>> 发送时间: 2016年5月26日 17:54:58
>> 收件人: freesurfer@nmr.mgh.harvard.edu
>> 主题: Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim
>>
>> It looks like it worked. there is not an error there. It did not find
>> any voxels above your chosen level of signficance, but that is not an
>> error per se
>>
>> On 05/26/2016 11:19 AM, Hao wen wrote:
>>> Doug:
>>>
>>> Thank you for your reply, it does not work, also, I think the problem
>>> is that for me after the clusterwise correction, I got no corrected
>>> cluster, I am not sure if it the problem that I set the --cache value
>>> and the --cwp value, but I changed the value, it always return me nothing!
>>>
>>> This is the msg, it said that found 0 value :
>>>
>>>
>>> Computing voxel-wise significance
>>> CSDpvalMaxSigMap(): found 0/163842 above 0
>>> Adjusting threshold for 1-tailed test.
>>> If the input is not a -log10(p) volume, re-run with --no-adjust.
>>> Searching for Clusters ...
>>> thmin=1.30 (0.998970), thmax=-1.00 (-1), thsignid=-1,
>>> minarea=0.00
>>> Found 2 clusters
>>> Max cluster size 132.153870
>>> Pruning by CW P-Value 0.001
>>> Saving thresholded output to
>>>lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh
>>> Saving cluster numbers to
>>> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh
>>> Saving cluster pval
>>> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh
>>>
>>>
>>> Do you have any idea?
>>>
>>> Best
>>>
>>> Hao
>>>
>>> 
>>> *发件人:* freesurfer-boun...@nmr.mgh.harvard.edu
>>>  代表 Douglas Greve
>>> 
>>> *发送时间:* 2016年5月26日 17:06:48
>>> *收件人:* freesurfer@nmr.mgh.harvard.edu
>>> *主题:* Re: [Freesurfer] Cluster-wise correction error with
>>> mri_glmfit-sim
>>> Instead of --2spaces, use--bonferroni 2
>>>
>>> On 5/26/16 10:30 AM, Hao wen wrote:
 Hello:

 Freesurfers, follow the tutorial '

 # FsTutorial 
 # GroupAnalysis
 ',
 my task is to find the thickness differences between
 groups(

Re: [Freesurfer] 答复: 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

[Douglas N Greve]

the sign is the expected sign of the contrast. If you do not have an 
apriori expectation as to what the sign is, then use abs (an unsigned 
test). Probably SurfStat uses pos. 4 = -log10(pthresh) sets the 
voxel-wise (ie, cluster forming threshold). You probably have to set a 
z-threshold for SurfStat; this equates to a p-value, which you then have 
to convert to -log10(p). Once the clusters are formed, then each cluster 
will have a size, and the probability (p-value) for that cluster. The 
--cwp thresh sets the threshold to filter out clusters that are not 
significant. Not that there is a difference between the cluster-forming 
threshold and the --cwp

On 05/26/2016 02:16 PM, Hao wen wrote:
> Hi, Doug:
> I find something, here r my command:
>
> mri_glmfit-sim \
>--glmdir lh.AD_CN_NO_COVARIATE.glmdir \
>--cache 4 pos \
>--cwp  0.05
>
> so I changed the sign, at first, it was 'neg', after correction, i got no 
> cluster, but with 'pos', I got  Ncluster = 9, and with 'abs', I got Ncluster 
> = 8, So i am a little lost, I checked out the explaination for the 
> 'mri_glmfit-sim ', so my question is that what is the differences for the 
> sign, and what are the thresholds for --cache and --cwp seperately? Hope to 
> hear from you soon!
> Merci
> Best
> Hao
> 
> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>  代表 Douglas N Greve 
> 
> 发送时间: 2016年5月26日 19:27:53
> 收件人: freesurfer@nmr.mgh.harvard.edu
> 主题: Re: [Freesurfer] 答复: 答复: 答复: Cluster-wise correction error with 
> mri_glmfit-sim
>
> They use two different methods. SurfStat uses gaussian random fields and
> FS uses monte carlo simulation. How significant is your cluster in FS?
>
> On 05/26/2016 01:17 PM, Hao wen wrote:
>> Hi:
>> Because I make the group analysis with SurfStat, and I get the cluster after 
>> the clusterwise correction, so I think in Freesurfer, we should have the 
>> similiar result:)
>>
>> 
>> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  代表 Douglas N Greve 
>> 
>> 发送时间: 2016年5月26日 18:22:58
>> 收件人: freesurfer@nmr.mgh.harvard.edu
>> 主题: Re: [Freesurfer] 答复: 答复: Cluster-wise correction error with 
>> mri_glmfit-sim
>>
>> why do you think there shold be a cluster?
>>
>> On 05/26/2016 12:21 PM, Hao wen wrote:
>>> Hi,
>>> I tried every value for the --cache and --cwp, as what i understood, the 
>>> --cache is the threshold for the vertex-wise correction and the --cwp is 
>>> the clusterwise correction, and i even tried the 0.99 with the --cwp, which 
>>> should give me all my cluster, but still, I got nothing, I checked the 
>>> 'mri_glmfit-sim', and it seems not so clear for me, do you there where is 
>>> the problem?
>>>
>>> Merci
>>> Hao
>>> 
>>> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  代表 Douglas N Greve 
>>> 
>>> 发送时间: 2016年5月26日 17:54:58
>>> 收件人: freesurfer@nmr.mgh.harvard.edu
>>> 主题: Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim
>>>
>>> It looks like it worked. there is not an error there. It did not find
>>> any voxels above your chosen level of signficance, but that is not an
>>> error per se
>>>
>>> On 05/26/2016 11:19 AM, Hao wen wrote:
 Doug:

 Thank you for your reply, it does not work, also, I think the problem
 is that for me after the clusterwise correction, I got no corrected
 cluster, I am not sure if it the problem that I set the --cache value
 and the --cwp value, but I changed the value, it always return me nothing!

 This is the msg, it said that found 0 value :


 Computing voxel-wise significance
 CSDpvalMaxSigMap(): found 0/163842 above 0
 Adjusting threshold for 1-tailed test.
 If the input is not a -log10(p) volume, re-run with --no-adjust.
 Searching for Clusters ...
 thmin=1.30 (0.998970), thmax=-1.00 (-1), thsignid=-1,
 minarea=0.00
 Found 2 clusters
 Max cluster size 132.153870
 Pruning by CW P-Value 0.001
 Saving thresholded output to
 lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh
 Saving cluster numbers to
 lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh
 Saving cluster pval
 lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh


 Do you have any idea?

 Best

 Hao

 
 *发件人:* freesurfer-boun...@nmr.mgh.harvard.edu
  代表 Douglas Greve
 
 *发送时间:* 2016年5月26日 17:06:48
 *收件人:* freesurfer@nmr.mgh.harvard.edu
 *主题:* Re: [Freesurfer] Cluster-wise correction error with
 mri_glmfit-sim
 Instead of --2spaces, use--bonferroni 2

 On 5/26/16 10:30 AM, Hao wen wrote:
> Hello:
>
> Freesurfers, follow the tutorial '
>
> # FsTutorial 
> # GroupAnalysis
> 

[Freesurfer] 答复: 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

[Hao wen]

Hi, Doug:
I find something, here r my command:

mri_glmfit-sim \
  --glmdir lh.AD_CN_NO_COVARIATE.glmdir \
  --cache 4 pos \
  --cwp  0.05

so I changed the sign, at first, it was 'neg', after correction, i got no 
cluster, but with 'pos', I got  Ncluster = 9, and with 'abs', I got Ncluster = 
8, So i am a little lost, I checked out the explaination for the 
'mri_glmfit-sim ', so my question is that what is the differences for the sign, 
and what are the thresholds for --cache and --cwp seperately? Hope to hear from 
you soon!
Merci
Best
Hao

发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Douglas N Greve 

发送时间: 2016年5月26日 19:27:53
收件人: freesurfer@nmr.mgh.harvard.edu
主题: Re: [Freesurfer] 答复: 答复: 答复: Cluster-wise correction error with 
mri_glmfit-sim

They use two different methods. SurfStat uses gaussian random fields and
FS uses monte carlo simulation. How significant is your cluster in FS?

On 05/26/2016 01:17 PM, Hao wen wrote:
> Hi:
> Because I make the group analysis with SurfStat, and I get the cluster after 
> the clusterwise correction, so I think in Freesurfer, we should have the 
> similiar result:)
>
> 
> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>  代表 Douglas N Greve 
> 
> 发送时间: 2016年5月26日 18:22:58
> 收件人: freesurfer@nmr.mgh.harvard.edu
> 主题: Re: [Freesurfer] 答复: 答复: Cluster-wise correction error with mri_glmfit-sim
>
> why do you think there shold be a cluster?
>
> On 05/26/2016 12:21 PM, Hao wen wrote:
>> Hi,
>> I tried every value for the --cache and --cwp, as what i understood, the 
>> --cache is the threshold for the vertex-wise correction and the --cwp is the 
>> clusterwise correction, and i even tried the 0.99 with the --cwp, which 
>> should give me all my cluster, but still, I got nothing, I checked the 
>> 'mri_glmfit-sim', and it seems not so clear for me, do you there where is 
>> the problem?
>>
>> Merci
>> Hao
>> 
>> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  代表 Douglas N Greve 
>> 
>> 发送时间: 2016年5月26日 17:54:58
>> 收件人: freesurfer@nmr.mgh.harvard.edu
>> 主题: Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim
>>
>> It looks like it worked. there is not an error there. It did not find
>> any voxels above your chosen level of signficance, but that is not an
>> error per se
>>
>> On 05/26/2016 11:19 AM, Hao wen wrote:
>>> Doug:
>>>
>>> Thank you for your reply, it does not work, also, I think the problem
>>> is that for me after the clusterwise correction, I got no corrected
>>> cluster, I am not sure if it the problem that I set the --cache value
>>> and the --cwp value, but I changed the value, it always return me nothing!
>>>
>>> This is the msg, it said that found 0 value :
>>>
>>>
>>> Computing voxel-wise significance
>>> CSDpvalMaxSigMap(): found 0/163842 above 0
>>> Adjusting threshold for 1-tailed test.
>>> If the input is not a -log10(p) volume, re-run with --no-adjust.
>>> Searching for Clusters ...
>>> thmin=1.30 (0.998970), thmax=-1.00 (-1), thsignid=-1,
>>> minarea=0.00
>>> Found 2 clusters
>>> Max cluster size 132.153870
>>> Pruning by CW P-Value 0.001
>>> Saving thresholded output to
>>>lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh
>>> Saving cluster numbers to
>>> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh
>>> Saving cluster pval
>>> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh
>>>
>>>
>>> Do you have any idea?
>>>
>>> Best
>>>
>>> Hao
>>>
>>> 
>>> *发件人:* freesurfer-boun...@nmr.mgh.harvard.edu
>>>  代表 Douglas Greve
>>> 
>>> *发送时间:* 2016年5月26日 17:06:48
>>> *收件人:* freesurfer@nmr.mgh.harvard.edu
>>> *主题:* Re: [Freesurfer] Cluster-wise correction error with
>>> mri_glmfit-sim
>>> Instead of --2spaces, use--bonferroni 2
>>>
>>> On 5/26/16 10:30 AM, Hao wen wrote:
 Hello:

 Freesurfers, follow the tutorial '

 # FsTutorial 
 # GroupAnalysis
 ',
 my task is to find the thickness differences between
 groups(Controls(30) & AD(30)),  and it works well for the first part
 which is to fit the linear model and get the uncorrected P_values,
 and I got the expected P-value map, but when  I followed the
 clusterwise correction for multiple comparision, with this command
 below:


 *mri_glmfit-sim \*
 *  --glmdir lh.gender_age.glmdir \*
 *  --cache 4 neg \*
 *  --cwp  0.05\*
 *  --2spaces*
 *
 *
 I got two questions:
 1) with the flag --2spaces, i got the error that this command not found;
 2) also, with or without the --2spaces, after the freeview open, i
 got another error, whic

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

[Hanbyul Cho]

Dear Douglas N Greve,


I sent again this design matrix (= Xg.dat) by attached.

Thank you.

Han.

On Thu, May 26, 2016 at 11:59 AM, Douglas N Greve  wrote:

> Design matrix, not contrast matrix. It was printed out as part of the
> terminal output. It can also be found in glmdir/Xg.dat
>
> On 05/26/2016 01:48 PM, Hanbyul Cho wrote:
> > Dear Douglas N Greve,
> >
> > The Contrast matrix was = [1 -1 0 0 0 0]
> > I attached the Xg.dat printed by unended mri_glmfit process.
> >
> > Thank you.
> >
> > Han.
> >
> > On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Please send the design matrix
> >
> > On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
> > > Dear Douglas N Greve,
> > >
> > > Today, I tested the previous group analysis on other computer,
> > and saw
> > > the same error massage.
> > >
> > > I attached the tested fsgd and mtx files.
> > >
> > > command:
> > > mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
> > > 052416_PA_CO_G2V2.fsgd dods --glmdir
> > > 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf fsaverage
> > lh --C
> > > 052416_contrast.mtx
> > >
> > > Thank you,
> > >
> > > Best wishes,
> > >
> > > Han
> > >
> > >
> > >
> > >
> > >
> > > On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve
> > > mailto:gr...@nmr.mgh.harvard.edu>
> >  > >> wrote:
> > >
> > > If you seek help with this problem, make sure to send:
> > >1. Your command line:
> > >  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
> > dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >2. The FSGD file (if using one)
> > >3. And the design matrix above
> > >
> > > On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > > > Dear FreeSurfer Team,
> > > >
> > > > I processed the Group analysis by FreeSurfer 5.3.0
> > > >
> > > > Our data has two groups (Patient, Control) and two
> > covariate values
> > > > (age, extra value)
> > > > mtx, contrast is 1 -1 0 0 0 0
> > > > The mris_preproc, and mri_surf2surf command were completed
> > > without error.
> > > >
> > > > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi
> > lh --meas
> > > > thickness --out lh.**G2V2.dods.mgh
> > > > mri_surf2surf --hemi lh --s fsaverage --sval
> > lh.**G2V2.dods.mgh
> > > --fwhm
> > > > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods
> --C
> > > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > > lh.**G2V2.dods_sm15.glmdir
> > > >
> > > > After mri_glmfit command, I saw the error message.
> > > >
> > > > =
> > > > ERROR: matrix is ill-conditioned or badly scaled, condno =
> > 1e+08
> > > > 
> > > > Possible problem with experimental design:
> > > > Check for duplicate entries and/or lack of range of
> > > > continuous variables within a class.
> > > > If you seek help with this problem, make sure to send:
> > > >   1. Your command line:
> > > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
> > dods --C
> > > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > > lh.**G2V2.dods_sm15.glmdir
> > > >   2. The FSGD file (if using one)
> > > >   3. And the design matrix above
> > > > =
> > > >
> > > > I think our fsgd and mtx compositions are equal to the
> > g2v2.fsgd
> > > which
> > > > FreeSurfer wiki example.
> > > > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
> > > >
> > > > In this situation, how can I correct my fsgd or mtx files?
> > Is there
> > > > any other command option?
> > > >
> > > > Best Regards,
> > > >
> > > > Han
> > > >
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > >  > >
> > > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center
> > > gr...@nmr.mgh.harvard.edu 
> > 

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

[Douglas N Greve]

Design matrix, not contrast matrix. It was printed out as part of the 
terminal output. It can also be found in glmdir/Xg.dat

On 05/26/2016 01:48 PM, Hanbyul Cho wrote:
> Dear Douglas N Greve,
>
> The Contrast matrix was = [1 -1 0 0 0 0]
> I attached the Xg.dat printed by unended mri_glmfit process.
>
> Thank you.
>
> Han.
>
> On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Please send the design matrix
>
> On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
> > Dear Douglas N Greve,
> >
> > Today, I tested the previous group analysis on other computer,
> and saw
> > the same error massage.
> >
> > I attached the tested fsgd and mtx files.
> >
> > command:
> > mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
> > 052416_PA_CO_G2V2.fsgd dods --glmdir
> > 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf fsaverage
> lh --C
> > 052416_contrast.mtx
> >
> > Thank you,
> >
> > Best wishes,
> >
> > Han
> >
> >
> >
> >
> >
> > On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
> >
> > If you seek help with this problem, make sure to send:
> >1. Your command line:
> >  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
> dods --C
> > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > lh.**G2V2.dods_sm15.glmdir
> >2. The FSGD file (if using one)
> >3. And the design matrix above
> >
> > On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > > Dear FreeSurfer Team,
> > >
> > > I processed the Group analysis by FreeSurfer 5.3.0
> > >
> > > Our data has two groups (Patient, Control) and two
> covariate values
> > > (age, extra value)
> > > mtx, contrast is 1 -1 0 0 0 0
> > > The mris_preproc, and mri_surf2surf command were completed
> > without error.
> > >
> > > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi
> lh --meas
> > > thickness --out lh.**G2V2.dods.mgh
> > > mri_surf2surf --hemi lh --s fsaverage --sval
> lh.**G2V2.dods.mgh
> > --fwhm
> > > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >
> > > After mri_glmfit command, I saw the error message.
> > >
> > > =
> > > ERROR: matrix is ill-conditioned or badly scaled, condno =
> 1e+08
> > > 
> > > Possible problem with experimental design:
> > > Check for duplicate entries and/or lack of range of
> > > continuous variables within a class.
> > > If you seek help with this problem, make sure to send:
> > >   1. Your command line:
> > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd
> dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >   2. The FSGD file (if using one)
> > >   3. And the design matrix above
> > > =
> > >
> > > I think our fsgd and mtx compositions are equal to the
> g2v2.fsgd
> > which
> > > FreeSurfer wiki example.
> > > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
> > >
> > > In this situation, how can I correct my fsgd or mtx files?
> Is there
> > > any other command option?
> > >
> > > Best Regards,
> > >
> > > Han
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> 
> >  >
> > >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@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.harvar

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

[Hanbyul Cho]

Dear Douglas N Greve,

The Contrast matrix was = [1 -1 0 0 0 0]
I attached the Xg.dat printed by unended mri_glmfit process.

Thank you.

Han.

On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve  wrote:

> Please send the design matrix
>
> On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
> > Dear Douglas N Greve,
> >
> > Today, I tested the previous group analysis on other computer, and saw
> > the same error massage.
> >
> > I attached the tested fsgd and mtx files.
> >
> > command:
> > mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd
> > 052416_PA_CO_G2V2.fsgd dods --glmdir
> > 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf fsaverage lh --C
> > 052416_contrast.mtx
> >
> > Thank you,
> >
> > Best wishes,
> >
> > Han
> >
> >
> >
> >
> >
> > On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve
> > mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > If you seek help with this problem, make sure to send:
> >1. Your command line:
> >  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > lh.**G2V2.dods_sm15.glmdir
> >2. The FSGD file (if using one)
> >3. And the design matrix above
> >
> > On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > > Dear FreeSurfer Team,
> > >
> > > I processed the Group analysis by FreeSurfer 5.3.0
> > >
> > > Our data has two groups (Patient, Control) and two covariate values
> > > (age, extra value)
> > > mtx, contrast is 1 -1 0 0 0 0
> > > The mris_preproc, and mri_surf2surf command were completed
> > without error.
> > >
> > > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi lh --meas
> > > thickness --out lh.**G2V2.dods.mgh
> > > mri_surf2surf --hemi lh --s fsaverage --sval lh.**G2V2.dods.mgh
> > --fwhm
> > > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >
> > > After mri_glmfit command, I saw the error message.
> > >
> > > =
> > > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> > > 
> > > Possible problem with experimental design:
> > > Check for duplicate entries and/or lack of range of
> > > continuous variables within a class.
> > > If you seek help with this problem, make sure to send:
> > >   1. Your command line:
> > > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > > lh.**G2V2.dods_sm15.glmdir
> > >   2. The FSGD file (if using one)
> > >   3. And the design matrix above
> > > =
> > >
> > > I think our fsgd and mtx compositions are equal to the g2v2.fsgd
> > which
> > > FreeSurfer wiki example.
> > > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
> > >
> > > In this situation, how can I correct my fsgd or mtx files? Is there
> > > any other command option?
> > >
> > > Best Regards,
> > >
> > > Han
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@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/
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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.
> >
> >
> >
> >
> > ___
> >

Re: [Freesurfer] 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

[Douglas N Greve]

They use two different methods. SurfStat uses gaussian random fields and 
FS uses monte carlo simulation. How significant is your cluster in FS?

On 05/26/2016 01:17 PM, Hao wen wrote:
> Hi:
> Because I make the group analysis with SurfStat, and I get the cluster after 
> the clusterwise correction, so I think in Freesurfer, we should have the 
> similiar result:)
>
> 
> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>  代表 Douglas N Greve 
> 
> 发送时间: 2016年5月26日 18:22:58
> 收件人: freesurfer@nmr.mgh.harvard.edu
> 主题: Re: [Freesurfer] 答复: 答复: Cluster-wise correction error with mri_glmfit-sim
>
> why do you think there shold be a cluster?
>
> On 05/26/2016 12:21 PM, Hao wen wrote:
>> Hi,
>> I tried every value for the --cache and --cwp, as what i understood, the 
>> --cache is the threshold for the vertex-wise correction and the --cwp is the 
>> clusterwise correction, and i even tried the 0.99 with the --cwp, which 
>> should give me all my cluster, but still, I got nothing, I checked the 
>> 'mri_glmfit-sim', and it seems not so clear for me, do you there where is 
>> the problem?
>>
>> Merci
>> Hao
>> 
>> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  代表 Douglas N Greve 
>> 
>> 发送时间: 2016年5月26日 17:54:58
>> 收件人: freesurfer@nmr.mgh.harvard.edu
>> 主题: Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim
>>
>> It looks like it worked. there is not an error there. It did not find
>> any voxels above your chosen level of signficance, but that is not an
>> error per se
>>
>> On 05/26/2016 11:19 AM, Hao wen wrote:
>>> Doug:
>>>
>>> Thank you for your reply, it does not work, also, I think the problem
>>> is that for me after the clusterwise correction, I got no corrected
>>> cluster, I am not sure if it the problem that I set the --cache value
>>> and the --cwp value, but I changed the value, it always return me nothing!
>>>
>>> This is the msg, it said that found 0 value :
>>>
>>>
>>> Computing voxel-wise significance
>>> CSDpvalMaxSigMap(): found 0/163842 above 0
>>> Adjusting threshold for 1-tailed test.
>>> If the input is not a -log10(p) volume, re-run with --no-adjust.
>>> Searching for Clusters ...
>>> thmin=1.30 (0.998970), thmax=-1.00 (-1), thsignid=-1,
>>> minarea=0.00
>>> Found 2 clusters
>>> Max cluster size 132.153870
>>> Pruning by CW P-Value 0.001
>>> Saving thresholded output to
>>>lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh
>>> Saving cluster numbers to
>>> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh
>>> Saving cluster pval
>>> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh
>>>
>>>
>>> Do you have any idea?
>>>
>>> Best
>>>
>>> Hao
>>>
>>> 
>>> *发件人:* freesurfer-boun...@nmr.mgh.harvard.edu
>>>  代表 Douglas Greve
>>> 
>>> *发送时间:* 2016年5月26日 17:06:48
>>> *收件人:* freesurfer@nmr.mgh.harvard.edu
>>> *主题:* Re: [Freesurfer] Cluster-wise correction error with
>>> mri_glmfit-sim
>>> Instead of --2spaces, use--bonferroni 2
>>>
>>> On 5/26/16 10:30 AM, Hao wen wrote:
 Hello:

 Freesurfers, follow the tutorial '

 # FsTutorial 
 # GroupAnalysis
 ',
 my task is to find the thickness differences between
 groups(Controls(30) & AD(30)),  and it works well for the first part
 which is to fit the linear model and get the uncorrected P_values,
 and I got the expected P-value map, but when  I followed the
 clusterwise correction for multiple comparision, with this command
 below:


 *mri_glmfit-sim \*
 *  --glmdir lh.gender_age.glmdir \*
 *  --cache 4 neg \*
 *  --cwp  0.05\*
 *  --2spaces*
 *
 *
 I got two questions:
 1) with the flag --2spaces, i got the error that this command not found;
 2) also, with or without the --2spaces, after the freeview open, i
 got another error, which said did not find any volume geometry
 information in the surface, I googled, and I know Doug has answered
 in this post:
 http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42911.html,
 but I think my freesurfer is the newest
 version:freesurfer-5.3.0-15052013-x86_64-centos!

 As below, these are my command and the output:

 *§§Command:*
 export
 SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
 cd $SUBJECTS_DIR/glm/AD_CN_NO_COVARIATE
 mri_glmfit-sim \
 --glmdir lh.AD_CN_NO_COVARIATE.glmdir \
 --cache 1.3 neg \
 --cwp  0.05\
 --2spaces

 # load the cluster annotation in freeview
 freeview -f
 $SUBJECTS_DIR/fsaverage/surf

[Freesurfer] 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

[Hao wen]

Hi:
Because I make the group analysis with SurfStat, and I get the cluster after 
the clusterwise correction, so I think in Freesurfer, we should have the 
similiar result:)


发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Douglas N Greve 

发送时间: 2016年5月26日 18:22:58
收件人: freesurfer@nmr.mgh.harvard.edu
主题: Re: [Freesurfer] 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

why do you think there shold be a cluster?

On 05/26/2016 12:21 PM, Hao wen wrote:
> Hi,
> I tried every value for the --cache and --cwp, as what i understood, the 
> --cache is the threshold for the vertex-wise correction and the --cwp is the 
> clusterwise correction, and i even tried the 0.99 with the --cwp, which 
> should give me all my cluster, but still, I got nothing, I checked the 
> 'mri_glmfit-sim', and it seems not so clear for me, do you there where is the 
> problem?
>
> Merci
> Hao
> 
> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>  代表 Douglas N Greve 
> 
> 发送时间: 2016年5月26日 17:54:58
> 收件人: freesurfer@nmr.mgh.harvard.edu
> 主题: Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim
>
> It looks like it worked. there is not an error there. It did not find
> any voxels above your chosen level of signficance, but that is not an
> error per se
>
> On 05/26/2016 11:19 AM, Hao wen wrote:
>> Doug:
>>
>> Thank you for your reply, it does not work, also, I think the problem
>> is that for me after the clusterwise correction, I got no corrected
>> cluster, I am not sure if it the problem that I set the --cache value
>> and the --cwp value, but I changed the value, it always return me nothing!
>>
>> This is the msg, it said that found 0 value :
>>
>>
>> Computing voxel-wise significance
>> CSDpvalMaxSigMap(): found 0/163842 above 0
>> Adjusting threshold for 1-tailed test.
>> If the input is not a -log10(p) volume, re-run with --no-adjust.
>> Searching for Clusters ...
>> thmin=1.30 (0.998970), thmax=-1.00 (-1), thsignid=-1,
>> minarea=0.00
>> Found 2 clusters
>> Max cluster size 132.153870
>> Pruning by CW P-Value 0.001
>> Saving thresholded output to
>>   lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh
>> Saving cluster numbers to
>> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh
>> Saving cluster pval
>> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh
>>
>>
>> Do you have any idea?
>>
>> Best
>>
>> Hao
>>
>> 
>> *发件人:* freesurfer-boun...@nmr.mgh.harvard.edu
>>  代表 Douglas Greve
>> 
>> *发送时间:* 2016年5月26日 17:06:48
>> *收件人:* freesurfer@nmr.mgh.harvard.edu
>> *主题:* Re: [Freesurfer] Cluster-wise correction error with
>> mri_glmfit-sim
>> Instead of --2spaces, use--bonferroni 2
>>
>> On 5/26/16 10:30 AM, Hao wen wrote:
>>> Hello:
>>>
>>> Freesurfers, follow the tutorial '
>>>
>>> # FsTutorial 
>>> # GroupAnalysis
>>> ',
>>> my task is to find the thickness differences between
>>> groups(Controls(30) & AD(30)),  and it works well for the first part
>>> which is to fit the linear model and get the uncorrected P_values,
>>> and I got the expected P-value map, but when  I followed the
>>> clusterwise correction for multiple comparision, with this command
>>> below:
>>>
>>>
>>> *mri_glmfit-sim \*
>>> *  --glmdir lh.gender_age.glmdir \*
>>> *  --cache 4 neg \*
>>> *  --cwp  0.05\*
>>> *  --2spaces*
>>> *
>>> *
>>> I got two questions:
>>> 1) with the flag --2spaces, i got the error that this command not found;
>>> 2) also, with or without the --2spaces, after the freeview open, i
>>> got another error, which said did not find any volume geometry
>>> information in the surface, I googled, and I know Doug has answered
>>> in this post:
>>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42911.html,
>>> but I think my freesurfer is the newest
>>> version:freesurfer-5.3.0-15052013-x86_64-centos!
>>>
>>> As below, these are my command and the output:
>>>
>>> *§§Command:*
>>> export
>>> SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
>>> cd $SUBJECTS_DIR/glm/AD_CN_NO_COVARIATE
>>> mri_glmfit-sim \
>>>--glmdir lh.AD_CN_NO_COVARIATE.glmdir \
>>>--cache 1.3 neg \
>>>--cwp  0.05\
>>>--2spaces
>>>
>>> # load the cluster annotation in freeview
>>> freeview -f
>>> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot
>>> -viewport 3d
>>>
>>>
>>> *§§Output:*
>>>
>>>
>>> cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd
>>> AD_CN_NO_COVARIATE.

Re: [Freesurfer] Design Matrix Creation

[Douglas N Greve]

Yes, create your matrix manually.

Those matrix lines are not quite right. The ages are in the correct 
column, but you need a 1 somewhere in columns 1-8 to indicate the class 
(ie, site/dx) that the subject is in.

On 05/26/2016 12:57 PM, Timothy Hendrickson wrote:
> Hi Doug,
>
> Thank you for such a prompt response. Just to be clear you are 
> recommending that I manually create the matrix file right?
>
> If so I want to ensure that I am understanding how to design the 
> matrix file properly.
>
> Let's imagine that the first participant is a control and is 13 and 
> the second is a patient and is 15. My understanding is that the matrix 
> file would be as follows:
> 0 0 0 0 0 0 0 0 13 0
> 0 0 0 0 0 0 0 0 0 15.
>
> -Tim
> Previous correspondences are below:
>
> You'll need a regressor for each of the 8 classes you describe below.
> You can use mri_glmfit to generate this (Xg.dat file)
> You'll need two more regressors for age, one for each diagnosis. If a
> subject (ie, row) is a control then the two values will be AGE 0. If the
> subject of the row is a patient, then the two values will be 0 AGE. You
> can then set up a Controls-Patients age (ie, interaction between dx and
> age) contrast like
> [0 0 0 0 0 0 0 0 1 -1]
> On 05/24/2016 02:30 PM, Timothy Hendrickson wrote:
> >
> > Freesurfer Support,
> >
> > I'd like to create a design matrix for a group analysis outside of the
> > DODS and DOSS models. I understand that in order to do this the -X
> > flag must be used. However, I have been unable to find examples of how
> > to do this.
> >
> > I am hoping to reveal a difference in thickness or gyrification
> > amongst a clinical population. The data set contains two factors:
> > diagnosis, and study site and one covariate: age. Diagnosis has two
> > levels: controls, and patients. Study site has four levels, one level
> > for each location the data has been collected from.
> >
> > What I would ideally like to do is:
> >
> > 1) Take into account offset differences amongst diagnosis and study site.
> >
> > 2) Allowing a difference in age slope amongst the diagnosis levels
> >
> > 3) Modeling the age slope as the same for the study site levels
> >
> > My FSGD file is designed as follows
> >
> > Class SITE 1-Control
> > Class SITE 1-PATIENT
> > Class SITE 2-Control
> > Class SITE 2-PATIENT
> > Class SITE 3-Control
> > Class SITE 3-PATIENT
> > Class SITE 4-Control
> > Class SITE 4-PATIENT
> > Variables age_at_scan
> >
> > study site levels = 1,2,3 and 4
> > diagnosis levels = PATIENT and Control
> > age_at_scan = covariate age
> >
> > Any advice would be greatly appreciated.
> >
> > Respectfully,
> >
> > Tim
> >
> > --
> > Timothy Hendrickson
> > Department of Psychiatry
> > University of Minnesota
> > Mobile: 507-259-3434  (texts okay)
> >
> >
> > ___
> > Freesurfer mailing list
> >Freesurfer@nmr.mgh.harvard.edu 
> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
> On Tue, May 24, 2016 at 1:30 PM, Timothy Hendrickson  > wrote:
>
>
> Freesurfer Support,
>
> I'd like to create a design matrix for a group analysis outside of
> the DODS and DOSS models. I understand that in order to do this
> the -X flag must be used. However, I have been unable to find
> examples of how to do this.
>
> I am hoping to reveal a difference in thickness or gyrification
> amongst a clinical population. The data set contains two factors:
> diagnosis, and study site and one covariate: age. Diagnosis has
> two levels: controls, and patients. Study site has four levels,
> one level for each location the data has been collected from.
>
> What I would ideally like to do is:
>
> 1) Take into account offset d

Re: [Freesurfer] glmdir question

[Douglas N Greve]

Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim


On 05/26/2016 12:53 PM, Clara Kühn wrote:
> Hi Doug,
>
> I ran this command with the --no-y Flag:
>   
> mri_glmfit-sim --glmdir 
> $SUBJECTS_DIR/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir
>  --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 abs --cwp 0.05 
> --2spaces --no-y
>
> and got the following error message:
>
> ERROR: Flag --no-y unrecognized.
> --glmdir 
> /scr/etsch2/kids/ct/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir
>  --cache-dir /scr/etsch2/kids/ct/average/mult-comp-cor --cache 3.0 abs --cwp 
> 0.05 --2spaces --no-y
>
> Does the flag need to be at a certain position?
> Thanks for your help
> Clara
>
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Donnerstag, 26. Mai 2016 17:53:47
> Betreff: Re: [Freesurfer] glmdir question
>
> By default it will compute a table. The rows of the table are each
> subject. The columns are the clusters. Each cell is the mean of the
> input for that subject over that cluster. It needs the input data to do
> this.
>
> On 05/26/2016 11:18 AM, Clara Kühn wrote:
>> I thought it had to be there because when I don't copy it into the glmdir I 
>> get an error message that it can't find the mgh in said glmdir.
>> I'm gonna try running it with the flag you mentioned.
>> What does it mean, though, that it won't compute means over the clusters?
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas Greve" 
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Donnerstag, 26. Mai 2016 17:15:41
>> Betreff: Re: [Freesurfer] glmdir question
>>
>> What is it doing in your glmdir? Usually you'd have it in another
>> location when running mri_glmfit (which creates the glmdir). In any
>> case, you can run it with --no-y and it will not look for the input file
>> (and will not compute means over the clusters).
>>
>> On 5/26/16 8:56 AM, Clara Kühn wrote:
>>> Dear FreeSurfer Experts,
>>>
>>> when running the Monte Carlo correction on a GLM I specify this command:
>>> mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp  0.05 
>>> --2spaces
>>>
>>> This assumes that my mgh file that I used as input for the GLM is in 
>>> lh.gender_age.glmdir. That means though, that everytime I calculate a GLM 
>>> and create a new folder for this GLM I have to copy the mgh file into the 
>>> glmdir to run the Monte Carlo correction. Is there a way to specify where 
>>> that mgh is located so that I don't have a bunch of copies of it in all my 
>>> glmdirs?
>>>
>>> Thanks for your help!
>>> Cheers
>>> Clara
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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.
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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
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Re: [Freesurfer] Design Matrix Creation

[Timothy Hendrickson]

Hi Doug,

Thank you for such a prompt response. Just to be clear you are recommending
that I manually create the matrix file right?

If so I want to ensure that I am understanding how to design the matrix
file properly.

Let's imagine that the first participant is a control and is 13 and the
second is a patient and is 15. My understanding is that the matrix file
would be as follows:
0 0 0 0 0 0 0 0 13 0
0 0 0 0 0 0 0 0 0 15.

-Tim

Previous correspondences are below:

You'll need a regressor for each of the 8 classes you describe below.
You can use mri_glmfit to generate this (Xg.dat file)
You'll need two more regressors for age, one for each diagnosis. If a
subject (ie, row) is a control then the two values will be AGE 0. If the
subject of the row is a patient, then the two values will be 0 AGE. You
can then set up a Controls-Patients age (ie, interaction between dx and
age) contrast like
[0 0 0 0 0 0 0 0 1 -1]

On 05/24/2016 02:30 PM, Timothy Hendrickson wrote:
>
> Freesurfer Support,
>
> I'd like to create a design matrix for a group analysis outside of the
> DODS and DOSS models. I understand that in order to do this the -X
> flag must be used. However, I have been unable to find examples of how
> to do this.
>
> I am hoping to reveal a difference in thickness or gyrification
> amongst a clinical population. The data set contains two factors:
> diagnosis, and study site and one covariate: age. Diagnosis has two
> levels: controls, and patients. Study site has four levels, one level
> for each location the data has been collected from.
>
> What I would ideally like to do is:
>
> 1) Take into account offset differences amongst diagnosis and study site.
>
> 2) Allowing a difference in age slope amongst the diagnosis levels
>
> 3) Modeling the age slope as the same for the study site levels
>
> My FSGD file is designed as follows
>
> Class SITE 1-Control
> Class SITE 1-PATIENT
> Class SITE 2-Control
> Class SITE 2-PATIENT
> Class SITE 3-Control
> Class SITE 3-PATIENT
> Class SITE 4-Control
> Class SITE 4-PATIENT
> Variables age_at_scan
>
> study site levels = 1,2,3 and 4
> diagnosis levels = PATIENT and Control
> age_at_scan = covariate age
>
> Any advice would be greatly appreciated.
>
> Respectfully,
>
> Tim
>
> --
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434  (texts okay)
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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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 athttp://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.



On Tue, May 24, 2016 at 1:30 PM, Timothy Hendrickson 
wrote:

>
> Freesurfer Support,
>
> I'd like to create a design matrix for a group analysis outside of the
> DODS and DOSS models. I understand that in order to do this the -X flag
> must be used. However, I have been unable to find examples of how to do
> this.
>
> I am hoping to reveal a difference in thickness or gyrification amongst a
> clinical population. The data set contains two factors: diagnosis, and
> study site and one covariate: age. Diagnosis has two levels: controls, and
> patients. Study site has four levels, one level for each location the data
> has been collected from.
>
> What I would ideally like to do is:
>
> 1) Take into account offset differences amongst diagnosis and study site.
>
> 2) Allowing a difference in age slope amongst the diagnosis levels
>
> 3) Modeling the age slope as the same for the study site levels
>
> My FSGD file is designed as follows
>
> Class SITE 1-Control
> Class SITE 1-PATIENT
> Class SITE 2-Control
> Class SITE 2-PATIENT
> Class SITE 3-Control
> Class SITE 3-PATIENT
> Class SITE 4-Control
> Class SITE 4-PATIENT
> Variables age_at_scan
>
> study site levels = 1,2,3 and 4
> diagnosis levels = PATIENT and Control
> age_at_scan = covariate age
>
> Any advice would be greatly appreciated.
>
> Respectfully,
>
> Tim
>
> --
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Mobile: 507-259-3434 (texts okay)
>



-- 
Timothy Hendrickson
Department of Psychiatry
University of 

Re: [Freesurfer] glmdir question

[Clara Kühn]

Hi Doug,

I ran this command with the --no-y Flag:
 
mri_glmfit-sim --glmdir 
$SUBJECTS_DIR/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir
 --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 abs --cwp 0.05 
--2spaces --no-y

and got the following error message:

ERROR: Flag --no-y unrecognized.
--glmdir 
/scr/etsch2/kids/ct/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir
 --cache-dir /scr/etsch2/kids/ct/average/mult-comp-cor --cache 3.0 abs --cwp 
0.05 --2spaces --no-y

Does the flag need to be at a certain position?
Thanks for your help
Clara


- Ursprüngliche Mail -
Von: "Douglas N Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 26. Mai 2016 17:53:47
Betreff: Re: [Freesurfer] glmdir question

By default it will compute a table. The rows of the table are each 
subject. The columns are the clusters. Each cell is the mean of the 
input for that subject over that cluster. It needs the input data to do 
this.

On 05/26/2016 11:18 AM, Clara Kühn wrote:
> I thought it had to be there because when I don't copy it into the glmdir I 
> get an error message that it can't find the mgh in said glmdir.
> I'm gonna try running it with the flag you mentioned.
> What does it mean, though, that it won't compute means over the clusters?
>
> - Ursprüngliche Mail -
> Von: "Douglas Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Donnerstag, 26. Mai 2016 17:15:41
> Betreff: Re: [Freesurfer] glmdir question
>
> What is it doing in your glmdir? Usually you'd have it in another
> location when running mri_glmfit (which creates the glmdir). In any
> case, you can run it with --no-y and it will not look for the input file
> (and will not compute means over the clusters).
>
> On 5/26/16 8:56 AM, Clara Kühn wrote:
>> Dear FreeSurfer Experts,
>>
>> when running the Monte Carlo correction on a GLM I specify this command:
>> mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp  0.05 
>> --2spaces
>>
>> This assumes that my mgh file that I used as input for the GLM is in 
>> lh.gender_age.glmdir. That means though, that everytime I calculate a GLM 
>> and create a new folder for this GLM I have to copy the mgh file into the 
>> glmdir to run the Monte Carlo correction. Is there a way to specify where 
>> that mgh is located so that I don't have a bunch of copies of it in all my 
>> glmdirs?
>>
>> Thanks for your help!
>> Cheers
>> Clara
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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
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[Freesurfer] (no subject)

[Saeed Mahdizadeh Bakhshmand]

Hello,

As we know, Freesurfer generates separate surface models and associated
labels for each brain hemisphere, is there any way to merge two hemisphere
and come up with a single cortex surface?

My best,
Saeed
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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 error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

[Douglas N Greve]

Please send the design matrix

On 05/24/2016 08:05 PM, Hanbyul Cho wrote:
> Dear Douglas N Greve,
>
> Today, I tested the previous group analysis on other computer, and saw 
> the same error massage.
>
> I attached the tested fsgd and mtx files.
>
> command:
> mri_glmfit --y 052416_lh.Pa_Co_G2V2_dods_sm15.mgh --fsgd 
> 052416_PA_CO_G2V2.fsgd dods --glmdir 
> 052416_lh.Pa_Co_G2V2_dods_sm15.glmdir --cortex --surf fsaverage lh --C 
> 052416_contrast.mtx
>
> Thank you,
>
> Best wishes,
>
> Han
>
>
>
>
>
> On Mon, May 23, 2016 at 12:56 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> If you seek help with this problem, make sure to send:
>1. Your command line:
>  mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> lh.**G2V2.dods_sm15.glmdir
>2. The FSGD file (if using one)
>3. And the design matrix above
>
> On 05/21/2016 04:57 PM, Hanbyul Cho wrote:
> > Dear FreeSurfer Team,
> >
> > I processed the Group analysis by FreeSurfer 5.3.0
> >
> > Our data has two groups (Patient, Control) and two covariate values
> > (age, extra value)
> > mtx, contrast is 1 -1 0 0 0 0
> > The mris_preproc, and mri_surf2surf command were completed
> without error.
> >
> > mris_preproc --fsgd **G2V2.fsgd --target fsaverage --hemi lh --meas
> > thickness --out lh.**G2V2.dods.mgh
> > mri_surf2surf --hemi lh --s fsaverage --sval lh.**G2V2.dods.mgh
> --fwhm
> > 15 --cortex --tval lh.**G2V2.dods_sm15.mgh
> > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > lh.**G2V2.dods_sm15.glmdir
> >
> > After mri_glmfit command, I saw the error message.
> >
> > =
> > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> > 
> > Possible problem with experimental design:
> > Check for duplicate entries and/or lack of range of
> > continuous variables within a class.
> > If you seek help with this problem, make sure to send:
> >   1. Your command line:
> > mri_glmfit --y lh.**G2V2.dods_sm15.mgh --fsgd **.fsgd dods --C
> > **G2V2.mtx --surf fsaverage lh --cortex --glmdir
> > lh.**G2V2.dods_sm15.glmdir
> >   2. The FSGD file (if using one)
> >   3. And the design matrix above
> > =
> >
> > I think our fsgd and mtx compositions are equal to the g2v2.fsgd
> which
> > FreeSurfer wiki example.
> > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V)
> >
> > In this situation, how can I correct my fsgd or mtx files? Is there
> > any other command option?
> >
> > Best Regards,
> >
> > Han
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

[Douglas N Greve]

why do you think there shold be a cluster?

On 05/26/2016 12:21 PM, Hao wen wrote:
> Hi,
> I tried every value for the --cache and --cwp, as what i understood, the 
> --cache is the threshold for the vertex-wise correction and the --cwp is the 
> clusterwise correction, and i even tried the 0.99 with the --cwp, which 
> should give me all my cluster, but still, I got nothing, I checked the 
> 'mri_glmfit-sim', and it seems not so clear for me, do you there where is the 
> problem?
>
> Merci
> Hao
> 
> 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
>  代表 Douglas N Greve 
> 
> 发送时间: 2016年5月26日 17:54:58
> 收件人: freesurfer@nmr.mgh.harvard.edu
> 主题: Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim
>
> It looks like it worked. there is not an error there. It did not find
> any voxels above your chosen level of signficance, but that is not an
> error per se
>
> On 05/26/2016 11:19 AM, Hao wen wrote:
>> Doug:
>>
>> Thank you for your reply, it does not work, also, I think the problem
>> is that for me after the clusterwise correction, I got no corrected
>> cluster, I am not sure if it the problem that I set the --cache value
>> and the --cwp value, but I changed the value, it always return me nothing!
>>
>> This is the msg, it said that found 0 value :
>>
>>
>> Computing voxel-wise significance
>> CSDpvalMaxSigMap(): found 0/163842 above 0
>> Adjusting threshold for 1-tailed test.
>> If the input is not a -log10(p) volume, re-run with --no-adjust.
>> Searching for Clusters ...
>> thmin=1.30 (0.998970), thmax=-1.00 (-1), thsignid=-1,
>> minarea=0.00
>> Found 2 clusters
>> Max cluster size 132.153870
>> Pruning by CW P-Value 0.001
>> Saving thresholded output to
>>   lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh
>> Saving cluster numbers to
>> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh
>> Saving cluster pval
>> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh
>>
>>
>> Do you have any idea?
>>
>> Best
>>
>> Hao
>>
>> 
>> *发件人:* freesurfer-boun...@nmr.mgh.harvard.edu
>>  代表 Douglas Greve
>> 
>> *发送时间:* 2016年5月26日 17:06:48
>> *收件人:* freesurfer@nmr.mgh.harvard.edu
>> *主题:* Re: [Freesurfer] Cluster-wise correction error with
>> mri_glmfit-sim
>> Instead of --2spaces, use--bonferroni 2
>>
>> On 5/26/16 10:30 AM, Hao wen wrote:
>>> Hello:
>>>
>>> Freesurfers, follow the tutorial '
>>>
>>> # FsTutorial 
>>> # GroupAnalysis
>>> ',
>>> my task is to find the thickness differences between
>>> groups(Controls(30) & AD(30)),  and it works well for the first part
>>> which is to fit the linear model and get the uncorrected P_values,
>>> and I got the expected P-value map, but when  I followed the
>>> clusterwise correction for multiple comparision, with this command
>>> below:
>>>
>>>
>>> *mri_glmfit-sim \*
>>> *  --glmdir lh.gender_age.glmdir \*
>>> *  --cache 4 neg \*
>>> *  --cwp  0.05\*
>>> *  --2spaces*
>>> *
>>> *
>>> I got two questions:
>>> 1) with the flag --2spaces, i got the error that this command not found;
>>> 2) also, with or without the --2spaces, after the freeview open, i
>>> got another error, which said did not find any volume geometry
>>> information in the surface, I googled, and I know Doug has answered
>>> in this post:
>>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42911.html,
>>> but I think my freesurfer is the newest
>>> version:freesurfer-5.3.0-15052013-x86_64-centos!
>>>
>>> As below, these are my command and the output:
>>>
>>> *§§Command:*
>>> export
>>> SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
>>> cd $SUBJECTS_DIR/glm/AD_CN_NO_COVARIATE
>>> mri_glmfit-sim \
>>>--glmdir lh.AD_CN_NO_COVARIATE.glmdir \
>>>--cache 1.3 neg \
>>>--cwp  0.05\
>>>--2spaces
>>>
>>> # load the cluster annotation in freeview
>>> freeview -f
>>> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot
>>> -viewport 3d
>>>
>>>
>>> *§§Output:*
>>>
>>>
>>> cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd
>>> AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh
>>> --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir
>>> SURFACE: fsaverage lh
>>> log file is lh.AD_CN_NO_COVARIATE.glmdir/cache.mri_glmfit-sim.log
>>>
>>> cd
>>> /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE
>>> /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/mri_glmfit-

[Freesurfer] 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

[Hao wen]

Hi,
I tried every value for the --cache and --cwp, as what i understood, the 
--cache is the threshold for the vertex-wise correction and the --cwp is the 
clusterwise correction, and i even tried the 0.99 with the --cwp, which should 
give me all my cluster, but still, I got nothing, I checked the 
'mri_glmfit-sim', and it seems not so clear for me, do you there where is the 
problem?

Merci
Hao

发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Douglas N Greve 

发送时间: 2016年5月26日 17:54:58
收件人: freesurfer@nmr.mgh.harvard.edu
主题: Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim

It looks like it worked. there is not an error there. It did not find
any voxels above your chosen level of signficance, but that is not an
error per se

On 05/26/2016 11:19 AM, Hao wen wrote:
>
> Doug:
>
> Thank you for your reply, it does not work, also, I think the problem
> is that for me after the clusterwise correction, I got no corrected
> cluster, I am not sure if it the problem that I set the --cache value
> and the --cwp value, but I changed the value, it always return me nothing!
>
> This is the msg, it said that found 0 value :
>
>
> Computing voxel-wise significance
> CSDpvalMaxSigMap(): found 0/163842 above 0
> Adjusting threshold for 1-tailed test.
> If the input is not a -log10(p) volume, re-run with --no-adjust.
> Searching for Clusters ...
> thmin=1.30 (0.998970), thmax=-1.00 (-1), thsignid=-1,
> minarea=0.00
> Found 2 clusters
> Max cluster size 132.153870
> Pruning by CW P-Value 0.001
> Saving thresholded output to
>  lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh
> Saving cluster numbers to
> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh
> Saving cluster pval
> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh
>
>
> Do you have any idea?
>
> Best
>
> Hao
>
> 
> *发件人:* freesurfer-boun...@nmr.mgh.harvard.edu
>  代表 Douglas Greve
> 
> *发送时间:* 2016年5月26日 17:06:48
> *收件人:* freesurfer@nmr.mgh.harvard.edu
> *主题:* Re: [Freesurfer] Cluster-wise correction error with
> mri_glmfit-sim
> Instead of --2spaces, use--bonferroni 2
>
> On 5/26/16 10:30 AM, Hao wen wrote:
>>
>> Hello:
>>
>> Freesurfers, follow the tutorial '
>>
>> # FsTutorial 
>> # GroupAnalysis
>> ',
>> my task is to find the thickness differences between
>> groups(Controls(30) & AD(30)),  and it works well for the first part
>> which is to fit the linear model and get the uncorrected P_values,
>> and I got the expected P-value map, but when  I followed the
>> clusterwise correction for multiple comparision, with this command
>> below:
>>
>>
>> *mri_glmfit-sim \*
>> *  --glmdir lh.gender_age.glmdir \*
>> *  --cache 4 neg \*
>> *  --cwp  0.05\*
>> *  --2spaces*
>> *
>> *
>> I got two questions:
>> 1) with the flag --2spaces, i got the error that this command not found;
>> 2) also, with or without the --2spaces, after the freeview open, i
>> got another error, which said did not find any volume geometry
>> information in the surface, I googled, and I know Doug has answered
>> in this post:
>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42911.html,
>> but I think my freesurfer is the newest
>> version:freesurfer-5.3.0-15052013-x86_64-centos!
>>
>> As below, these are my command and the output:
>>
>> *§§Command:*
>> export
>> SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
>> cd $SUBJECTS_DIR/glm/AD_CN_NO_COVARIATE
>> mri_glmfit-sim \
>>   --glmdir lh.AD_CN_NO_COVARIATE.glmdir \
>>   --cache 1.3 neg \
>>   --cwp  0.05\
>>   --2spaces
>>
>> # load the cluster annotation in freeview
>> freeview -f
>> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot
>> -viewport 3d
>>
>>
>> *§§Output:*
>>
>>
>> cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd
>> AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh
>> --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir
>> SURFACE: fsaverage lh
>> log file is lh.AD_CN_NO_COVARIATE.glmdir/cache.mri_glmfit-sim.log
>>
>> cd
>> /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE
>> /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/mri_glmfit-sim
>> --glmdir lh.AD_CN_NO_COVARIATE.glmdir --cache 1.3 neg --cwp 0.05
>>
>> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
>> Thu May 26 16:20:39 CEST 2016
>> Linux HP1973 3.11.0-26-generic #45~precise1-Ubuntu SMP T

Re: [Freesurfer] mri_glmfit version

[Douglas N Greve]

I don't know of any difference that would have caused this, though it 
has been a long time since 5.1. The 0.3 shift is suspicious because that 
is the difference between a signed test and an unsigned test in 
log10(p). Can you capture the screen output from the two runs and send 
them to me?


On 05/26/2016 09:09 AM, Victor Montal Blancafort wrote:
> Dear FS experts
>
> We have been playing around with different mri_glmfit versions. I 
> processed all my data with FS v5.1, and then I run the mri_glmfit with 
> both the 5.1 and 5.3 versions, using exactly the same X, same 
> contrasts matrix and obviously the same images. Our concern is that 
> the results differ significantly between both versions. Concretely, 
> the results from the 5.3 mri_glmfit version are shifted 0.3 points 
> with respect from the 5.1 one. More precisely, the results using the 
> 5.1 version at 1.0 look the same as the 5.3 at 1.3 significance level.
>
> Is there any difference in parameter estimation or anything else 
> between both versions? Should the results be the same given that we 
> use the same data, parameters, etc?
>
> Thanks in advance for your replies,
>
> Best regards,
>
> V.
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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
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Re: [Freesurfer] Connectivity design ill-conditioned

[Douglas N Greve]

It is strange that it has 47 columns, I would have expected 48, however, 
the current problem is caused by the wm.dat and vcsf.dat having the same 
content. Probably it was an error when you set up the command line for  
fcseed-config


On 05/25/2016 06:40 PM, Zimmerman, Jared Perry wrote:
> Hi, I'm having a problem running first level connectivity analysis on 
> my resting-state data.  When I run selxavg3-sess I keep getting a 
> notice that my design is ill-conditioned but I can't figure out why.  
> I am trying to run analysis on two 124 volume rsfMRI runs in my fsd 
> and the design matrix looks fine to me with dimensions 248x47 
> (although should ncols be an even number since I'm doing two runs?).
>
> Poking around the Xtmp.mat I noticed a few things that are confusing.  
> Notably, flac.funcfspec points only to one of my runs in the fsd, and 
> flac.X is a 124x24 matrix which appears to be the design matrix for 
> just one of my runs (and if there are 24 columns in that, should there 
> be 28 columns in the design matrix for combining both runs?).  Any 
> help figuring out why this design is ill-conditioned would be great.
>
> I've attached my Xtmp.mat, selxavg3.log and analysis design file to 
> this email, but it's unclear to me if the mailing list will scrub them 
> off.  If so I can make them available some other way.
>
>
> Thanks,
> Jared
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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/

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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] glmdir question

[Douglas N Greve]

By default it will compute a table. The rows of the table are each 
subject. The columns are the clusters. Each cell is the mean of the 
input for that subject over that cluster. It needs the input data to do 
this.

On 05/26/2016 11:18 AM, Clara Kühn wrote:
> I thought it had to be there because when I don't copy it into the glmdir I 
> get an error message that it can't find the mgh in said glmdir.
> I'm gonna try running it with the flag you mentioned.
> What does it mean, though, that it won't compute means over the clusters?
>
> - Ursprüngliche Mail -
> Von: "Douglas Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Donnerstag, 26. Mai 2016 17:15:41
> Betreff: Re: [Freesurfer] glmdir question
>
> What is it doing in your glmdir? Usually you'd have it in another
> location when running mri_glmfit (which creates the glmdir). In any
> case, you can run it with --no-y and it will not look for the input file
> (and will not compute means over the clusters).
>
> On 5/26/16 8:56 AM, Clara Kühn wrote:
>> Dear FreeSurfer Experts,
>>
>> when running the Monte Carlo correction on a GLM I specify this command:
>> mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp  0.05 
>> --2spaces
>>
>> This assumes that my mgh file that I used as input for the GLM is in 
>> lh.gender_age.glmdir. That means though, that everytime I calculate a GLM 
>> and create a new folder for this GLM I have to copy the mgh file into the 
>> glmdir to run the Monte Carlo correction. Is there a way to specify where 
>> that mgh is located so that I don't have a bunch of copies of it in all my 
>> glmdirs?
>>
>> Thanks for your help!
>> Cheers
>> Clara
>>
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> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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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>
>

-- 
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MGH-NMR Center
gr...@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
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Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim

[Douglas N Greve]

It looks like it worked. there is not an error there. It did not find 
any voxels above your chosen level of signficance, but that is not an 
error per se

On 05/26/2016 11:19 AM, Hao wen wrote:
>
> Doug:
>
> Thank you for your reply, it does not work, also, I think the problem 
> is that for me after the clusterwise correction, I got no corrected 
> cluster, I am not sure if it the problem that I set the --cache value 
> and the --cwp value, but I changed the value, it always return me nothing!
>
> This is the msg, it said that found 0 value :
>
>
> Computing voxel-wise significance
> CSDpvalMaxSigMap(): found 0/163842 above 0
> Adjusting threshold for 1-tailed test.
> If the input is not a -log10(p) volume, re-run with --no-adjust.
> Searching for Clusters ...
> thmin=1.30 (0.998970), thmax=-1.00 (-1), thsignid=-1, 
> minarea=0.00
> Found 2 clusters
> Max cluster size 132.153870
> Pruning by CW P-Value 0.001
> Saving thresholded output to 
>  lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh
> Saving cluster numbers to 
> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh
> Saving cluster pval 
> lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh
>
>
> Do you have any idea?
>
> Best
>
> Hao
>
> 
> *发件人:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  代表 Douglas Greve 
> 
> *发送时间:* 2016年5月26日 17:06:48
> *收件人:* freesurfer@nmr.mgh.harvard.edu
> *主题:* Re: [Freesurfer] Cluster-wise correction error with 
> mri_glmfit-sim
> Instead of --2spaces, use--bonferroni 2
>
> On 5/26/16 10:30 AM, Hao wen wrote:
>>
>> Hello:
>>
>> Freesurfers, follow the tutorial '
>>
>> # FsTutorial 
>> # GroupAnalysis 
>> ',
>>  
>> my task is to find the thickness differences between 
>> groups(Controls(30) & AD(30)),  and it works well for the first part 
>> which is to fit the linear model and get the uncorrected P_values, 
>> and I got the expected P-value map, but when  I followed the 
>> clusterwise correction for multiple comparision, with this command 
>> below:
>>
>>
>> *mri_glmfit-sim \*
>> *  --glmdir lh.gender_age.glmdir \*
>> *  --cache 4 neg \*
>> *  --cwp  0.05\*
>> *  --2spaces*
>> *
>> *
>> I got two questions:
>> 1) with the flag --2spaces, i got the error that this command not found;
>> 2) also, with or without the --2spaces, after the freeview open, i 
>> got another error, which said did not find any volume geometry 
>> information in the surface, I googled, and I know Doug has answered 
>> in this post:
>> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42911.html, 
>> but I think my freesurfer is the newest 
>> version:freesurfer-5.3.0-15052013-x86_64-centos!
>>
>> As below, these are my command and the output:
>>
>> *§§Command:*
>> export 
>> SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
>> cd $SUBJECTS_DIR/glm/AD_CN_NO_COVARIATE
>> mri_glmfit-sim \
>>   --glmdir lh.AD_CN_NO_COVARIATE.glmdir \
>>   --cache 1.3 neg \
>>   --cwp  0.05\
>>   --2spaces
>>
>> # load the cluster annotation in freeview
>> freeview -f 
>> $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot
>>  
>> -viewport 3d
>>
>>
>> *§§Output:*
>>
>>
>> cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd 
>> AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh 
>> --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir
>> SURFACE: fsaverage lh
>> log file is lh.AD_CN_NO_COVARIATE.glmdir/cache.mri_glmfit-sim.log
>>
>> cd 
>> /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE
>> /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/mri_glmfit-sim
>> --glmdir lh.AD_CN_NO_COVARIATE.glmdir --cache 1.3 neg --cwp 0.05
>>
>> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
>> Thu May 26 16:20:39 CEST 2016
>> Linux HP1973 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 
>> 04:02:35 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
>> wen
>> setenv SUBJECTS_DIR 
>> /aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
>> FREESURFER_HOME 
>> /aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos
>>
>> Original mri_glmfit command line:
>> cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd 
>> AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh 
>> --cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir
>>
>> DoSim = 0
>> UseCache = 1
>> DoPoll = 0
>> DoPBSubmit = 0
>> DoBackground 

[Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim

[Hao wen]

Doug:

Thank you for your reply, it does not work, also, I think the problem is that 
for me after the clusterwise correction, I got no corrected cluster, I am not 
sure if it the problem that I set the --cache value and the --cwp value, but I 
changed the value, it always return me nothing!

This is the msg, it said that found 0 value :


Computing voxel-wise significance
CSDpvalMaxSigMap(): found 0/163842 above 0
Adjusting threshold for 1-tailed test.
If the input is not a -log10(p) volume, re-run with --no-adjust.
Searching for Clusters ...
thmin=1.30 (0.998970), thmax=-1.00 (-1), thsignid=-1, minarea=0.00
Found 2 clusters
Max cluster size 132.153870
Pruning by CW P-Value 0.001
Saving thresholded output to  
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh
Saving cluster numbers to 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh
Saving cluster pval 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh



Do you have any idea?

Best

Hao


发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
 代表 Douglas Greve 

发送时间: 2016年5月26日 17:06:48
收件人: freesurfer@nmr.mgh.harvard.edu
主题: Re: [Freesurfer] Cluster-wise correction error with mri_glmfit-sim

Instead of --2spaces, use--bonferroni 2

On 5/26/16 10:30 AM, Hao wen wrote:

Hello:

Freesurfers, follow the tutorial '

  *   FsTutorial
  *   
GroupAnalysis',
 my task is to find the thickness differences between groups(Controls(30) & 
AD(30)),  and it works well for the first part which is to fit the linear model 
and get the uncorrected P_values, and I got the expected P-value map, but when  
I followed the clusterwise correction for multiple comparision, with this 
command below:


mri_glmfit-sim \
  --glmdir lh.gender_age.glmdir \
  --cache 4 neg \
  --cwp  0.05\
  --2spaces

I got two questions:
1) with the flag --2spaces, i got the error that this command not found;
2) also, with or without the --2spaces, after the freeview open, i got another 
error, which said did not find any volume geometry information in the surface, 
I googled, and I know Doug has answered in this post:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42911.html, but 
I think my freesurfer is the newest 
version:freesurfer-5.3.0-15052013-x86_64-centos!

As below, these are my command and the output:

§§Command:
export 
SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
cd $SUBJECTS_DIR/glm/AD_CN_NO_COVARIATE
mri_glmfit-sim \
  --glmdir lh.AD_CN_NO_COVARIATE.glmdir \
  --cache 1.3 neg \
  --cwp  0.05\
  --2spaces

# load the cluster annotation in freeview
freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot
 -viewport 3d



§§Output:


cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd 
AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex 
--glmdir lh.AD_CN_NO_COVARIATE.glmdir
SURFACE: fsaverage lh
log file is lh.AD_CN_NO_COVARIATE.glmdir/cache.mri_glmfit-sim.log

cd 
/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/mri_glmfit-sim
--glmdir lh.AD_CN_NO_COVARIATE.glmdir --cache 1.3 neg --cwp 0.05

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Thu May 26 16:20:39 CEST 2016
Linux HP1973 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 
2014 x86_64 x86_64 x86_64 GNU/Linux
wen
setenv SUBJECTS_DIR 
/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
FREESURFER_HOME 
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos

Original mri_glmfit command line:
cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd 
AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex 
--glmdir lh.AD_CN_NO_COVARIATE.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 22.776285
CSD 
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd
mri_surfcluster --in lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh --csd 
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd
 --mask lh.AD_CN_NO_COVARIATE.glmdir/mask.mgh --cwsig 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh --vwsig 
lh.AD_CN_NO_COVARIATE.glm

Re: [Freesurfer] glmdir question

[Clara Kühn]

I thought it had to be there because when I don't copy it into the glmdir I get 
an error message that it can't find the mgh in said glmdir.
I'm gonna try running it with the flag you mentioned.
What does it mean, though, that it won't compute means over the clusters? 

- Ursprüngliche Mail -
Von: "Douglas Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 26. Mai 2016 17:15:41
Betreff: Re: [Freesurfer] glmdir question

What is it doing in your glmdir? Usually you'd have it in another 
location when running mri_glmfit (which creates the glmdir). In any 
case, you can run it with --no-y and it will not look for the input file 
(and will not compute means over the clusters).

On 5/26/16 8:56 AM, Clara Kühn wrote:
> Dear FreeSurfer Experts,
>
> when running the Monte Carlo correction on a GLM I specify this command:
> mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp  0.05 
> --2spaces
>
> This assumes that my mgh file that I used as input for the GLM is in 
> lh.gender_age.glmdir. That means though, that everytime I calculate a GLM and 
> create a new folder for this GLM I have to copy the mgh file into the glmdir 
> to run the Monte Carlo correction. Is there a way to specify where that mgh 
> is located so that I don't have a bunch of copies of it in all my glmdirs?
>
> Thanks for your help!
> Cheers
> Clara
>

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Re: [Freesurfer] New to Freesurfer; cortical thickness

[Bruce Fischl]

you have to run them separately
On Fri, 27 May 2016, Marja Caverlé wrote:


Thanks! It runs now. But that still leaves me with the question whether I
can do all the patients in one run or that I have to run them separately.

Best,

Marja

On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé 
wrote:
  Thanks Bruce,

  001 was indeed the subject id, but I did not know it needed -s.
  If I don't specify the output directory, where will it be put?

  Best,

  Marja

On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl
 wrote:
  the subject id is something you make up. What is 001 in
  your example? Maybe it is the subject ID? If so, preface
  it with -s. You probably also want to specify the location
  of your output directory with -sd 

  cheers
  Bruce

  On Fri, 27 May 2016, Marja Caverlé wrote:

Hi Bruce,

Thank you for your response. I tried it many
times and I kept getting the
same error like at the bottom of this email.
Why do you put the -s in there? and what
exactly is the subject ID? FYI, I
was already in the folder where the .nii.gz is
located.  And by your answer
I assume I can do it only one patient at a
time?

Thanks,

Marja

---
Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all
-001 -i AD_TM001.nii.gz -all

ERROR: Flag -001 unrecognized.

-001 -i AD_TM001.nii.gz -all

Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin
Kernel Version 15.4.0: Fri Feb
26 22:08:05 PST 2016;
root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Thu May 26
14:40:06 AEST 2016


For more details, see the log file 

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
---


On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl

wrote:
      Hi Marja

      can you send us the actual command and
screen output you ran? It
      should be something like:

      recon-all -all -s  -i 

      Depending on your hardware it will take
hours to finish, but it
      will do pretty much everything
(segmentation, surface
      reconstruction, template registration,
thickness measurement,
      parcellation, etc...)

       cheers
      Bruce

      On Thu, 26 May 2016, Marja Caverlé
wrote:

            Hi All,

            I am new to Freesurfer and I would
like to use it
            for a project I am working
            on right now. For this project I
have two patient
            groups of which I have
            structural MRI scans and a lot of
other measures. I
            hope to get cortical
            thickness numbers from the scans
and compare these
            with the other measures.

            Anyway, I am trying to get
something done in
            Freesurfer and it does not
            really seem to work. I assume I
have to do a
            recon-all -all, but when I try
            this, I get an error saying that
the flag is
            unrecognised. It probably is a
            small error, easy to solve, but I
already get stuck
            on it since I am totally
            new to Freesurfer.

            Could anyone help me out?
            Some of my questions are;

            - Am I correct that recon-all -all
already
            coregisters the scans to
            template?
            - What will be the outcome? Will I
get pictures, or
            a table with numbers,
            and if it is a table, which area's
are specified? I
            have a list of ROIs, but
            how do I let Freesurfer know I am
interested in
            those areas?
            - Can I do recon-all -all on a
folder with all my
            patients, or do I have to
            do it one by one? (There not that
much,
            approximately 12 scans)
            - Can I do recon-all -all on
.nii.gz files? The
            originals are DICOM, but the
            problem is that there is just one
 

Re: [Freesurfer] glmdir question

[Douglas Greve]

What is it doing in your glmdir? Usually you'd have it in another 
location when running mri_glmfit (which creates the glmdir). In any 
case, you can run it with --no-y and it will not look for the input file 
(and will not compute means over the clusters).

On 5/26/16 8:56 AM, Clara Kühn wrote:
> Dear FreeSurfer Experts,
>
> when running the Monte Carlo correction on a GLM I specify this command:
> mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp  0.05 
> --2spaces
>
> This assumes that my mgh file that I used as input for the GLM is in 
> lh.gender_age.glmdir. That means though, that everytime I calculate a GLM and 
> create a new folder for this GLM I have to copy the mgh file into the glmdir 
> to run the Monte Carlo correction. Is there a way to specify where that mgh 
> is located so that I don't have a bunch of copies of it in all my glmdirs?
>
> Thanks for your help!
> Cheers
> Clara
>

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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] New to Freesurfer; cortical thickness

[Bruce Fischl]

whatever then environment variable SUBJECTS_DIR points to
On Fri, 27 May 
2016, Marja Caverlé wrote:



Thanks Bruce,

001 was indeed the subject id, but I did not know it needed -s.
If I don't specify the output directory, where will it be put?

Best,

Marja

On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl 
wrote:
  the subject id is something you make up. What is 001 in your
  example? Maybe it is the subject ID? If so, preface it with -s.
  You probably also want to specify the location of your output
  directory with -sd 

  cheers
  Bruce

  On Fri, 27 May 2016, Marja Caverlé wrote:

Hi Bruce,

Thank you for your response. I tried it many times
and I kept getting the
same error like at the bottom of this email.
Why do you put the -s in there? and what exactly is
the subject ID? FYI, I
was already in the folder where the .nii.gz is
located.  And by your answer
I assume I can do it only one patient at a time?

Thanks,

Marja

---
Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001
-i AD_TM001.nii.gz -all

ERROR: Flag -001 unrecognized.

-001 -i AD_TM001.nii.gz -all

Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel
Version 15.4.0: Fri Feb
26 22:08:05 PST 2016;
root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Thu May 26
14:40:06 AEST 2016


For more details, see the log file 

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
---


On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl

wrote:
      Hi Marja

      can you send us the actual command and screen
output you ran? It
      should be something like:

      recon-all -all -s  -i 

      Depending on your hardware it will take hours
to finish, but it
      will do pretty much everything (segmentation,
surface
      reconstruction, template registration,
thickness measurement,
      parcellation, etc...)

       cheers
      Bruce

      On Thu, 26 May 2016, Marja Caverlé wrote:

            Hi All,

            I am new to Freesurfer and I would like
to use it
            for a project I am working
            on right now. For this project I have
two patient
            groups of which I have
            structural MRI scans and a lot of other
measures. I
            hope to get cortical
            thickness numbers from the scans and
compare these
            with the other measures.

            Anyway, I am trying to get something
done in
            Freesurfer and it does not
            really seem to work. I assume I have to
do a
            recon-all -all, but when I try
            this, I get an error saying that the
flag is
            unrecognised. It probably is a
            small error, easy to solve, but I
already get stuck
            on it since I am totally
            new to Freesurfer.

            Could anyone help me out?
            Some of my questions are;

            - Am I correct that recon-all -all
already
            coregisters the scans to
            template?
            - What will be the outcome? Will I get
pictures, or
            a table with numbers,
            and if it is a table, which area's are
specified? I
            have a list of ROIs, but
            how do I let Freesurfer know I am
interested in
            those areas?
            - Can I do recon-all -all on a folder
with all my
            patients, or do I have to
            do it one by one? (There not that much,
            approximately 12 scans)
            - Can I do recon-all -all on .nii.gz
files? The
            originals are DICOM, but the
            problem is that there is just one large
DICOM
            folder, which does not specify
            which files are part of which scan. I
have converted
            them to .nii.gz since I
            am a bit familiar 

Re: [Freesurfer] New to Freesurfer; cortical thickness

[Douglas Greve]

If you don't give it a -s option, the program will not run and there 
will not be any output


On 5/26/16 10:43 AM, Marja Caverlé wrote:

Thanks Bruce,

001 was indeed the subject id, but I did not know it needed -s.
If I don't specify the output directory, where will it be put?

Best,

Marja

On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:


the subject id is something you make up. What is 001 in your
example? Maybe it is the subject ID? If so, preface it with -s.
You probably also want to specify the location of your output
directory with -sd 

cheers
Bruce


On Fri, 27 May 2016, Marja Caverlé wrote:

Hi Bruce,

Thank you for your response. I tried it many times and I kept
getting the
same error like at the bottom of this email.
Why do you put the -s in there? and what exactly is the
subject ID? FYI, I
was already in the folder where the .nii.gz is located.  And
by your answer
I assume I can do it only one patient at a time?

Thanks,

Marja

---
Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i
AD_TM001.nii.gz -all

ERROR: Flag -001 unrecognized.

-001 -i AD_TM001.nii.gz -all

Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version
15.4.0: Fri Feb
26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Thu May 26 14:40:06 AEST 2016


For more details, see the log file

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
---


On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>>
wrote:
  Hi Marja

  can you send us the actual command and screen output you
ran? It
  should be something like:

  recon-all -all -s  -i 

  Depending on your hardware it will take hours to finish,
but it
  will do pretty much everything (segmentation, surface
  reconstruction, template registration, thickness
measurement,
  parcellation, etc...)

   cheers
  Bruce

  On Thu, 26 May 2016, Marja Caverlé wrote:

Hi All,

I am new to Freesurfer and I would like to use it
for a project I am working
on right now. For this project I have two patient
groups of which I have
structural MRI scans and a lot of other measures. I
hope to get cortical
thickness numbers from the scans and compare these
with the other measures.

Anyway, I am trying to get something done in
Freesurfer and it does not
really seem to work. I assume I have to do a
recon-all -all, but when I try
this, I get an error saying that the flag is
unrecognised. It probably is a
small error, easy to solve, but I already get stuck
on it since I am totally
new to Freesurfer.

Could anyone help me out?
Some of my questions are;

- Am I correct that recon-all -all already
coregisters the scans to
template?
- What will be the outcome? Will I get pictures, or
a table with numbers,
and if it is a table, which area's are specified? I
have a list of ROIs, but
how do I let Freesurfer know I am interested in
those areas?
- Can I do recon-all -all on a folder with all my
patients, or do I have to
do it one by one? (There not that much,
approximately 12 scans)
- Can I do recon-all -all on .nii.gz files? The
originals are DICOM, but the
problem is that there is just one large DICOM
folder, which does not specify
which files are part of which scan. I have converted
them to .nii.gz since I
am a bit familiar with FSL, but I do not know
whether this actually works in
Freesurfer.
- Why do I get the unrecognised flag error?

I apologise for these questions, they are probably
very easy to answer, but
I just don't have a clue yet.

Thank you guys.

Best,

Marja

Re: [Freesurfer] request for corrected p-values for mni305 space

[Douglas Greve]

What do you mean? There is a way to correct with mri_glmfit-sim using 
the --grf option.


On 5/25/16 9:25 PM, Joseph Dien wrote:

Hi,
   just a user request for corrected p-values for the mni305 space 
analyses (i.e., sig.voxel.nii.gz files).


Thanks!

Joe



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com 
Cell Phone: 202-297-8117
http://joedien.com



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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
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Cluster-wise correction error with mri_glmfit-sim

[Douglas Greve]

Instead of --2spaces, use--bonferroni 2

On 5/26/16 10:30 AM, Hao wen wrote:


Hello:

Freesurfers, follow the tutorial '

# FsTutorial 
# GroupAnalysis 
', 
my task is to find the thickness differences between 
groups(Controls(30) & AD(30)),  and it works well for the first part 
which is to fit the linear model and get the uncorrected P_values, and 
I got the expected P-value map, but when  I followed the clusterwise 
correction for multiple comparision, with this command below:



*mri_glmfit-sim \*
*  --glmdir lh.gender_age.glmdir \*
*  --cache 4 neg \*
*  --cwp  0.05\*
*  --2spaces*
*
*
I got two questions:
1) with the flag --2spaces, i got the error that this command not found;
2) also, with or without the --2spaces, after the freeview open, i got 
another error, which said did not find any volume geometry information 
in the surface, I googled, and I know Doug has answered in this post:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42911.html, 
but I think my freesurfer is the newest 
version:freesurfer-5.3.0-15052013-x86_64-centos!


As below, these are my command and the output:

*§§Command:*
export 
SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/

cd $SUBJECTS_DIR/glm/AD_CN_NO_COVARIATE
mri_glmfit-sim \
  --glmdir lh.AD_CN_NO_COVARIATE.glmdir \
  --cache 1.3 neg \
  --cwp  0.05\
  --2spaces

# load the cluster annotation in freeview
freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot 
-viewport 3d



*§§Output:*


cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd 
AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh 
--cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir

SURFACE: fsaverage lh
log file is lh.AD_CN_NO_COVARIATE.glmdir/cache.mri_glmfit-sim.log

cd 
/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE

/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/mri_glmfit-sim
--glmdir lh.AD_CN_NO_COVARIATE.glmdir --cache 1.3 neg --cwp 0.05

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Thu May 26 16:20:39 CEST 2016
Linux HP1973 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 
04:02:35 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

wen
setenv SUBJECTS_DIR 
/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
FREESURFER_HOME 
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos


Original mri_glmfit command line:
cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd 
AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh 
--cortex --glmdir lh.AD_CN_NO_COVARIATE.glmdir


DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 22.776285
CSD 
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd
mri_surfcluster --in lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh 
--csd 
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd 
--mask lh.AD_CN_NO_COVARIATE.glmdir/mask.mgh --cwsig 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh 
--vwsig 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.voxel.mgh 
--sum 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.summary 
--ocn 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh 
--oannot 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot 
--annot aparc --csdpdf 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.pdf.dat 
--cwpvalthresh 0.05 --o 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh 
--no-fixmni --surf white

Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
hemi   = lh
srcid  = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 1.3
thmax  = -1
fdr= -1
minarea= 0
xfmfile= talairach.xfm
nth = -1
outid= 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh MGH
ocnid= 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh MGH
sumfile  = 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.summary
subjectsdir= 
/aramis/dataARAMIS/

Re: [Freesurfer] New to Freesurfer; cortical thickness

[Marja Caverlé]

Thanks Douglas!

On Fri, May 27, 2016 at 1:02 AM, Douglas Greve 
wrote:

> run them separately
>
> On 5/26/16 11:01 AM, Marja Caverlé wrote:
>
> Thanks! It runs now. But that still leaves me with the question whether I
> can do all the patients in one run or that I have to run them separately.
>
> Best,
>
> Marja
>
> On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé 
> wrote:
>
>> Thanks Bruce,
>>
>> 001 was indeed the subject id, but I did not know it needed -s.
>> If I don't specify the output directory, where will it be put?
>>
>> Best,
>>
>> Marja
>>
>> On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>>
>>> the subject id is something you make up. What is 001 in your example?
>>> Maybe it is the subject ID? If so, preface it with -s. You probably also
>>> want to specify the location of your output directory with -sd >> where you will put each subject>
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Fri, 27 May 2016, Marja Caverlé wrote:
>>>
>>> Hi Bruce,

 Thank you for your response. I tried it many times and I kept getting
 the
 same error like at the bottom of this email.
 Why do you put the -s in there? and what exactly is the subject ID?
 FYI, I
 was already in the folder where the .nii.gz is located.  And by your
 answer
 I assume I can do it only one patient at a time?

 Thanks,

 Marja

 ---
 Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz
 -all

 ERROR: Flag -001 unrecognized.

 -001 -i AD_TM001.nii.gz -all

 Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0:
 Fri Feb
 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64


 recon-all -s  exited with ERRORS at Thu May 26 14:40:06 AEST 2016


 For more details, see the log file

 To report a problem, see
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
 ---


 On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl <
 fis...@nmr.mgh.harvard.edu>
 wrote:
   Hi Marja

   can you send us the actual command and screen output you ran? It
   should be something like:

   recon-all -all -s  -i 

   Depending on your hardware it will take hours to finish, but it
   will do pretty much everything (segmentation, surface
   reconstruction, template registration, thickness measurement,
   parcellation, etc...)

cheers
   Bruce

   On Thu, 26 May 2016, Marja Caverlé wrote:

 Hi All,

 I am new to Freesurfer and I would like to use it
 for a project I am working
 on right now. For this project I have two patient
 groups of which I have
 structural MRI scans and a lot of other measures. I
 hope to get cortical
 thickness numbers from the scans and compare these
 with the other measures.

 Anyway, I am trying to get something done in
 Freesurfer and it does not
 really seem to work. I assume I have to do a
 recon-all -all, but when I try
 this, I get an error saying that the flag is
 unrecognised. It probably is a
 small error, easy to solve, but I already get stuck
 on it since I am totally
 new to Freesurfer.

 Could anyone help me out?
 Some of my questions are;

 - Am I correct that recon-all -all already
 coregisters the scans to
 template?
 - What will be the outcome? Will I get pictures, or
 a table with numbers,
 and if it is a table, which area's are specified? I
 have a list of ROIs, but
 how do I let Freesurfer know I am interested in
 those areas?
 - Can I do recon-all -all on a folder with all my
 patients, or do I have to
 do it one by one? (There not that much,
 approximately 12 scans)
 - Can I do recon-all -all on .nii.gz files? The
 originals are DICOM, but the
 problem is that there is just one large DICOM
 folder, which does not specify
 which files are part of which scan. I have converted
 them to .nii.gz since I
 am a bit familiar with FSL, but I do not know
 whether this actually works in
 Freesurfer.
 - Why do I get the unrecognised flag error?

 I apologise for these questions, they are probably
 very easy to answer, but
 I just don't have a clue

Re: [Freesurfer] New to Freesurfer; cortical thickness

[Douglas Greve]

run them separately

On 5/26/16 11:01 AM, Marja Caverlé wrote:
Thanks! It runs now. But that still leaves me with the question 
whether I can do all the patients in one run or that I have to run 
them separately.


Best,

Marja

On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé 
mailto:marja.cave...@gmail.com>> wrote:


Thanks Bruce,

001 was indeed the subject id, but I did not know it needed -s.
If I don't specify the output directory, where will it be put?

Best,

Marja

On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>>
wrote:

the subject id is something you make up. What is 001 in your
example? Maybe it is the subject ID? If so, preface it with
-s. You probably also want to specify the location of your
output directory with -sd 

cheers
Bruce


On Fri, 27 May 2016, Marja Caverlé wrote:

Hi Bruce,

Thank you for your response. I tried it many times and I
kept getting the
same error like at the bottom of this email.
Why do you put the -s in there? and what exactly is the
subject ID? FYI, I
was already in the folder where the .nii.gz is located. 
And by your answer

I assume I can do it only one patient at a time?

Thanks,

Marja

---
Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i
AD_TM001.nii.gz -all

ERROR: Flag -001 unrecognized.

-001 -i AD_TM001.nii.gz -all

Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel
Version 15.4.0: Fri Feb
26 22:08:05 PST 2016;
root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Thu May 26 14:40:06
AEST 2016


For more details, see the log file

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
---


On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl
mailto:fis...@nmr.mgh.harvard.edu>>
wrote:
  Hi Marja

  can you send us the actual command and screen output
you ran? It
  should be something like:

  recon-all -all -s  -i 

  Depending on your hardware it will take hours to
finish, but it
  will do pretty much everything (segmentation, surface
  reconstruction, template registration, thickness
measurement,
  parcellation, etc...)

   cheers
  Bruce

  On Thu, 26 May 2016, Marja Caverlé wrote:

Hi All,

I am new to Freesurfer and I would like to use it
for a project I am working
on right now. For this project I have two patient
groups of which I have
structural MRI scans and a lot of other
measures. I
hope to get cortical
thickness numbers from the scans and compare these
with the other measures.

Anyway, I am trying to get something done in
Freesurfer and it does not
really seem to work. I assume I have to do a
recon-all -all, but when I try
this, I get an error saying that the flag is
unrecognised. It probably is a
small error, easy to solve, but I already get
stuck
on it since I am totally
new to Freesurfer.

Could anyone help me out?
Some of my questions are;

- Am I correct that recon-all -all already
coregisters the scans to
template?
- What will be the outcome? Will I get
pictures, or
a table with numbers,
and if it is a table, which area's are
specified? I
have a list of ROIs, but
how do I let Freesurfer know I am interested in
those areas?
- Can I do recon-all -all on a folder with all my
patients, or do I have to
do it one by one? (There not that much,
approximately 12 scans)
- Can I do recon-all -all on .nii.gz files? The
originals are DICOM, but the
problem is that there is just one large DICOM
folder, which does n

Re: [Freesurfer] New to Freesurfer; cortical thickness

[Marja Caverlé]

Thanks! It runs now. But that still leaves me with the question whether I
can do all the patients in one run or that I have to run them separately.

Best,

Marja

On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé 
wrote:

> Thanks Bruce,
>
> 001 was indeed the subject id, but I did not know it needed -s.
> If I don't specify the output directory, where will it be put?
>
> Best,
>
> Marja
>
> On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl  > wrote:
>
>> the subject id is something you make up. What is 001 in your example?
>> Maybe it is the subject ID? If so, preface it with -s. You probably also
>> want to specify the location of your output directory with -sd > where you will put each subject>
>>
>> cheers
>> Bruce
>>
>>
>> On Fri, 27 May 2016, Marja Caverlé wrote:
>>
>> Hi Bruce,
>>>
>>> Thank you for your response. I tried it many times and I kept getting the
>>> same error like at the bottom of this email.
>>> Why do you put the -s in there? and what exactly is the subject ID? FYI,
>>> I
>>> was already in the folder where the .nii.gz is located.  And by your
>>> answer
>>> I assume I can do it only one patient at a time?
>>>
>>> Thanks,
>>>
>>> Marja
>>>
>>> ---
>>> Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz
>>> -all
>>>
>>> ERROR: Flag -001 unrecognized.
>>>
>>> -001 -i AD_TM001.nii.gz -all
>>>
>>> Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri
>>> Feb
>>> 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64
>>>
>>>
>>> recon-all -s  exited with ERRORS at Thu May 26 14:40:06 AEST 2016
>>>
>>>
>>> For more details, see the log file
>>>
>>> To report a problem, see
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
>>> ---
>>>
>>>
>>> On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu>
>>> wrote:
>>>   Hi Marja
>>>
>>>   can you send us the actual command and screen output you ran? It
>>>   should be something like:
>>>
>>>   recon-all -all -s  -i 
>>>
>>>   Depending on your hardware it will take hours to finish, but it
>>>   will do pretty much everything (segmentation, surface
>>>   reconstruction, template registration, thickness measurement,
>>>   parcellation, etc...)
>>>
>>>cheers
>>>   Bruce
>>>
>>>   On Thu, 26 May 2016, Marja Caverlé wrote:
>>>
>>> Hi All,
>>>
>>> I am new to Freesurfer and I would like to use it
>>> for a project I am working
>>> on right now. For this project I have two patient
>>> groups of which I have
>>> structural MRI scans and a lot of other measures. I
>>> hope to get cortical
>>> thickness numbers from the scans and compare these
>>> with the other measures.
>>>
>>> Anyway, I am trying to get something done in
>>> Freesurfer and it does not
>>> really seem to work. I assume I have to do a
>>> recon-all -all, but when I try
>>> this, I get an error saying that the flag is
>>> unrecognised. It probably is a
>>> small error, easy to solve, but I already get stuck
>>> on it since I am totally
>>> new to Freesurfer.
>>>
>>> Could anyone help me out?
>>> Some of my questions are;
>>>
>>> - Am I correct that recon-all -all already
>>> coregisters the scans to
>>> template?
>>> - What will be the outcome? Will I get pictures, or
>>> a table with numbers,
>>> and if it is a table, which area's are specified? I
>>> have a list of ROIs, but
>>> how do I let Freesurfer know I am interested in
>>> those areas?
>>> - Can I do recon-all -all on a folder with all my
>>> patients, or do I have to
>>> do it one by one? (There not that much,
>>> approximately 12 scans)
>>> - Can I do recon-all -all on .nii.gz files? The
>>> originals are DICOM, but the
>>> problem is that there is just one large DICOM
>>> folder, which does not specify
>>> which files are part of which scan. I have converted
>>> them to .nii.gz since I
>>> am a bit familiar with FSL, but I do not know
>>> whether this actually works in
>>> Freesurfer.
>>> - Why do I get the unrecognised flag error?
>>>
>>> I apologise for these questions, they are probably
>>> very easy to answer, but
>>> I just don't have a clue yet.
>>>
>>> Thank you guys.
>>>
>>> Best,
>>>
>>> Marja
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The inform

Re: [Freesurfer] New to Freesurfer; cortical thickness

[Marja Caverlé]

Thanks Bruce,

001 was indeed the subject id, but I did not know it needed -s.
If I don't specify the output directory, where will it be put?

Best,

Marja

On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl 
wrote:

> the subject id is something you make up. What is 001 in your example?
> Maybe it is the subject ID? If so, preface it with -s. You probably also
> want to specify the location of your output directory with -sd  where you will put each subject>
>
> cheers
> Bruce
>
>
> On Fri, 27 May 2016, Marja Caverlé wrote:
>
> Hi Bruce,
>>
>> Thank you for your response. I tried it many times and I kept getting the
>> same error like at the bottom of this email.
>> Why do you put the -s in there? and what exactly is the subject ID? FYI, I
>> was already in the folder where the .nii.gz is located.  And by your
>> answer
>> I assume I can do it only one patient at a time?
>>
>> Thanks,
>>
>> Marja
>>
>> ---
>> Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz
>> -all
>>
>> ERROR: Flag -001 unrecognized.
>>
>> -001 -i AD_TM001.nii.gz -all
>>
>> Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri
>> Feb
>> 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64
>>
>>
>> recon-all -s  exited with ERRORS at Thu May 26 14:40:06 AEST 2016
>>
>>
>> For more details, see the log file
>>
>> To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
>> ---
>>
>>
>> On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   Hi Marja
>>
>>   can you send us the actual command and screen output you ran? It
>>   should be something like:
>>
>>   recon-all -all -s  -i 
>>
>>   Depending on your hardware it will take hours to finish, but it
>>   will do pretty much everything (segmentation, surface
>>   reconstruction, template registration, thickness measurement,
>>   parcellation, etc...)
>>
>>cheers
>>   Bruce
>>
>>   On Thu, 26 May 2016, Marja Caverlé wrote:
>>
>> Hi All,
>>
>> I am new to Freesurfer and I would like to use it
>> for a project I am working
>> on right now. For this project I have two patient
>> groups of which I have
>> structural MRI scans and a lot of other measures. I
>> hope to get cortical
>> thickness numbers from the scans and compare these
>> with the other measures.
>>
>> Anyway, I am trying to get something done in
>> Freesurfer and it does not
>> really seem to work. I assume I have to do a
>> recon-all -all, but when I try
>> this, I get an error saying that the flag is
>> unrecognised. It probably is a
>> small error, easy to solve, but I already get stuck
>> on it since I am totally
>> new to Freesurfer.
>>
>> Could anyone help me out?
>> Some of my questions are;
>>
>> - Am I correct that recon-all -all already
>> coregisters the scans to
>> template?
>> - What will be the outcome? Will I get pictures, or
>> a table with numbers,
>> and if it is a table, which area's are specified? I
>> have a list of ROIs, but
>> how do I let Freesurfer know I am interested in
>> those areas?
>> - Can I do recon-all -all on a folder with all my
>> patients, or do I have to
>> do it one by one? (There not that much,
>> approximately 12 scans)
>> - Can I do recon-all -all on .nii.gz files? The
>> originals are DICOM, but the
>> problem is that there is just one large DICOM
>> folder, which does not specify
>> which files are part of which scan. I have converted
>> them to .nii.gz since I
>> am a bit familiar with FSL, but I do not know
>> whether this actually works in
>> Freesurfer.
>> - Why do I get the unrecognised flag error?
>>
>> I apologise for these questions, they are probably
>> very easy to answer, but
>> I just don't have a clue yet.
>>
>> Thank you guys.
>>
>> Best,
>>
>> Marja
>>
>>
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 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 co

Re: [Freesurfer] New to Freesurfer; cortical thickness

[Bruce Fischl]

the subject id is something you make up. What is 001 in your example? 
Maybe it is the subject ID? If so, preface it with -s. You probably also 
want to specify the location of your output directory with -sd where you will put each subject>


cheers
Bruce

On Fri, 27 May 2016, Marja Caverlé wrote:


Hi Bruce,

Thank you for your response. I tried it many times and I kept getting the
same error like at the bottom of this email.
Why do you put the -s in there? and what exactly is the subject ID? FYI, I
was already in the folder where the .nii.gz is located.  And by your answer
I assume I can do it only one patient at a time?

Thanks,

Marja

---
Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all

ERROR: Flag -001 unrecognized.

-001 -i AD_TM001.nii.gz -all

Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb
26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Thu May 26 14:40:06 AEST 2016


For more details, see the log file 

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
---


On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl 
wrote:
  Hi Marja

  can you send us the actual command and screen output you ran? It
  should be something like:

  recon-all -all -s  -i 

  Depending on your hardware it will take hours to finish, but it
  will do pretty much everything (segmentation, surface
  reconstruction, template registration, thickness measurement,
  parcellation, etc...)

   cheers
  Bruce

  On Thu, 26 May 2016, Marja Caverlé wrote:

Hi All,

I am new to Freesurfer and I would like to use it
for a project I am working
on right now. For this project I have two patient
groups of which I have
structural MRI scans and a lot of other measures. I
hope to get cortical
thickness numbers from the scans and compare these
with the other measures.

Anyway, I am trying to get something done in
Freesurfer and it does not
really seem to work. I assume I have to do a
recon-all -all, but when I try
this, I get an error saying that the flag is
unrecognised. It probably is a
small error, easy to solve, but I already get stuck
on it since I am totally
new to Freesurfer.

Could anyone help me out?
Some of my questions are;

- Am I correct that recon-all -all already
coregisters the scans to
template?
- What will be the outcome? Will I get pictures, or
a table with numbers,
and if it is a table, which area's are specified? I
have a list of ROIs, but
how do I let Freesurfer know I am interested in
those areas?
- Can I do recon-all -all on a folder with all my
patients, or do I have to
do it one by one? (There not that much,
approximately 12 scans)
- Can I do recon-all -all on .nii.gz files? The
originals are DICOM, but the
problem is that there is just one large DICOM
folder, which does not specify
which files are part of which scan. I have converted
them to .nii.gz since I
am a bit familiar with FSL, but I do not know
whether this actually works in
Freesurfer.
- Why do I get the unrecognised flag error?

I apologise for these questions, they are probably
very easy to answer, but
I just don't have a clue yet.

Thank you guys.

Best,

Marja







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e-mail
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dis

[Freesurfer] Cluster-wise correction error with mri_glmfit-sim

[Hao wen]

Hello:

Freesurfers, follow the tutorial '

  *   FsTutorial
  *   
GroupAnalysis',
 my task is to find the thickness differences between groups(Controls(30) & 
AD(30)),  and it works well for the first part which is to fit the linear model 
and get the uncorrected P_values, and I got the expected P-value map, but when  
I followed the clusterwise correction for multiple comparision, with this 
command below:


mri_glmfit-sim \
  --glmdir lh.gender_age.glmdir \
  --cache 4 neg \
  --cwp  0.05\
  --2spaces

I got two questions:
1) with the flag --2spaces, i got the error that this command not found;
2) also, with or without the --2spaces, after the freeview open, i got another 
error, which said did not find any volume geometry information in the surface, 
I googled, and I know Doug has answered in this post:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42911.html, but 
I think my freesurfer is the newest 
version:freesurfer-5.3.0-15052013-x86_64-centos!

As below, these are my command and the output:

§§Command:
export 
SUBJECTS_DIR=/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
cd $SUBJECTS_DIR/glm/AD_CN_NO_COVARIATE
mri_glmfit-sim \
  --glmdir lh.AD_CN_NO_COVARIATE.glmdir \
  --cache 1.3 neg \
  --cwp  0.05\
  --2spaces

# load the cluster annotation in freeview
freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot
 -viewport 3d



§§Output:


cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd 
AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex 
--glmdir lh.AD_CN_NO_COVARIATE.glmdir
SURFACE: fsaverage lh
log file is lh.AD_CN_NO_COVARIATE.glmdir/cache.mri_glmfit-sim.log

cd 
/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/glm/AD_CN_NO_COVARIATE
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/mri_glmfit-sim
--glmdir lh.AD_CN_NO_COVARIATE.glmdir --cache 1.3 neg --cwp 0.05

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Thu May 26 16:20:39 CEST 2016
Linux HP1973 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 
2014 x86_64 x86_64 x86_64 GNU/Linux
wen
setenv SUBJECTS_DIR 
/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
FREESURFER_HOME 
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos

Original mri_glmfit command line:
cmdline mri_glmfit --y lh.AD_CN_NO_COVARIATE.thickness.15.mgh --fsgd 
AD_CN_NO_COVARIATE.fsgd dods --C group.diff.mtx --surf fsaverage lh --cortex 
--glmdir lh.AD_CN_NO_COVARIATE.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 22.776285
CSD 
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd
mri_surfcluster --in lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh --csd 
/aramis/dartagnan2/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/average/mult-comp-cor/fsaverage/lh/cortex/fwhm23/neg/th13/mc-z.csd
 --mask lh.AD_CN_NO_COVARIATE.glmdir/mask.mgh --cwsig 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.mgh --vwsig 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.voxel.mgh --sum 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.summary 
--ocn lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh 
--oannot lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.annot 
--annot aparc --csdpdf 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.pdf.dat --cwpvalthresh 
0.05 --o lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh 
--no-fixmni --surf white
Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
hemi   = lh
srcid  = lh.AD_CN_NO_COVARIATE.glmdir/group.diff/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 1.3
thmax  = -1
fdr= -1
minarea= 0
xfmfile= talairach.xfm
nth = -1
outid= 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.masked.mgh MGH
ocnid= lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.ocn.mgh 
MGH
sumfile  = 
lh.AD_CN_NO_COVARIATE.glmdir/group.diff/cache.th13.neg.sig.cluster.summary
subjectsdir= 
/aramis/dataARAMIS/users/junhao.wen/Back_up/Data_AD_CN/ADNI_60_AD_CN_object_recon_all_output/
FixMNI = 0
Found 149955 vertices in

Re: [Freesurfer] New to Freesurfer; cortical thickness

[Marja Caverlé]

Hi Bruce,

Thank you for your response. I tried it many times and I kept getting the
same error like at the bottom of this email.
Why do you put the -s in there? and what exactly is the subject ID? FYI, I
was already in the folder where the .nii.gz is located.  And by your answer
I assume I can do it only one patient at a time?

Thanks,

Marja

---
Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all

ERROR: Flag -001 unrecognized.

-001 -i AD_TM001.nii.gz -all

Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri
Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64


recon-all -s  exited with ERRORS at Thu May 26 14:40:06 AEST 2016


For more details, see the log file

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
---

On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl 
wrote:

> Hi Marja
>
> can you send us the actual command and screen output you ran? It should be
> something like:
>
> recon-all -all -s  -i 
>
> Depending on your hardware it will take hours to finish, but it will do
> pretty much everything (segmentation, surface reconstruction, template
> registration, thickness measurement, parcellation, etc...)
>
>  cheers
> Bruce
>
>
> On Thu, 26 May 2016, Marja Caverlé wrote:
>
> Hi All,
>>
>> I am new to Freesurfer and I would like to use it for a project I am
>> working
>> on right now. For this project I have two patient groups of which I have
>> structural MRI scans and a lot of other measures. I hope to get cortical
>> thickness numbers from the scans and compare these with the other
>> measures.
>>
>> Anyway, I am trying to get something done in Freesurfer and it does not
>> really seem to work. I assume I have to do a recon-all -all, but when I
>> try
>> this, I get an error saying that the flag is unrecognised. It probably is
>> a
>> small error, easy to solve, but I already get stuck on it since I am
>> totally
>> new to Freesurfer.
>>
>> Could anyone help me out?
>> Some of my questions are;
>>
>> - Am I correct that recon-all -all already coregisters the scans to
>> template?
>> - What will be the outcome? Will I get pictures, or a table with numbers,
>> and if it is a table, which area's are specified? I have a list of ROIs,
>> but
>> how do I let Freesurfer know I am interested in those areas?
>> - Can I do recon-all -all on a folder with all my patients, or do I have
>> to
>> do it one by one? (There not that much, approximately 12 scans)
>> - Can I do recon-all -all on .nii.gz files? The originals are DICOM, but
>> the
>> problem is that there is just one large DICOM folder, which does not
>> specify
>> which files are part of which scan. I have converted them to .nii.gz
>> since I
>> am a bit familiar with FSL, but I do not know whether this actually works
>> in
>> Freesurfer.
>> - Why do I get the unrecognised flag error?
>>
>> I apologise for these questions, they are probably very easy to answer,
>> but
>> I just don't have a clue yet.
>>
>> Thank you guys.
>>
>> Best,
>>
>> Marja
>>
>>
>>
>>
>>
>>
>>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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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[Freesurfer] mri_glmfit version

[Victor Montal Blancafort]

Dear FS experts

We have been playing around with different mri_glmfit versions. I processed
all my data with FS v5.1, and then I run the mri_glmfit with both the 5.1
and 5.3 versions, using exactly the same X, same contrasts matrix and
obviously the same images. Our concern is that the results differ
significantly between both versions. Concretely, the results from the 5.3
mri_glmfit version are shifted 0.3 points with respect from the 5.1 one.
More precisely, the results using the 5.1 version at 1.0 look the same as
the 5.3 at 1.3 significance level.

Is there any difference in parameter estimation or anything else between
both versions? Should the results be the same given that we use the same
data, parameters, etc?

Thanks in advance for your replies,

Best regards,

V.
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] New to Freesurfer; cortical thickness

[Bruce Fischl]

Hi Marja

can you send us the actual command and screen output you ran? It should 
be something like:


recon-all -all -s  -i 

Depending on your hardware it will take hours to finish, but it will do 
pretty much everything (segmentation, surface reconstruction, template 
registration, thickness measurement, parcellation, etc...)


 cheers
Bruce

On Thu, 26 May 2016, Marja Caverlé wrote:


Hi All,

I am new to Freesurfer and I would like to use it for a project I am working
on right now. For this project I have two patient groups of which I have
structural MRI scans and a lot of other measures. I hope to get cortical
thickness numbers from the scans and compare these with the other measures.

Anyway, I am trying to get something done in Freesurfer and it does not
really seem to work. I assume I have to do a recon-all -all, but when I try
this, I get an error saying that the flag is unrecognised. It probably is a
small error, easy to solve, but I already get stuck on it since I am totally
new to Freesurfer.

Could anyone help me out?
Some of my questions are;

- Am I correct that recon-all -all already coregisters the scans to
template?
- What will be the outcome? Will I get pictures, or a table with numbers,
and if it is a table, which area's are specified? I have a list of ROIs, but
how do I let Freesurfer know I am interested in those areas?
- Can I do recon-all -all on a folder with all my patients, or do I have to
do it one by one? (There not that much, approximately 12 scans)
- Can I do recon-all -all on .nii.gz files? The originals are DICOM, but the
problem is that there is just one large DICOM folder, which does not specify
which files are part of which scan. I have converted them to .nii.gz since I
am a bit familiar with FSL, but I do not know whether this actually works in
Freesurfer.
- Why do I get the unrecognised flag error?

I apologise for these questions, they are probably very easy to answer, but
I just don't have a clue yet.

Thank you guys.

Best,

Marja






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[Freesurfer] glmdir question

[Clara Kühn]

Dear FreeSurfer Experts,

when running the Monte Carlo correction on a GLM I specify this command:
mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp  0.05 --2spaces

This assumes that my mgh file that I used as input for the GLM is in 
lh.gender_age.glmdir. That means though, that everytime I calculate a GLM and 
create a new folder for this GLM I have to copy the mgh file into the glmdir to 
run the Monte Carlo correction. Is there a way to specify where that mgh is 
located so that I don't have a bunch of copies of it in all my glmdirs?

Thanks for your help!
Cheers
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] recon-all on 0.5mm scan?

[Falk Lüsebrink]

Hi Trisanna,

you can find instructions on how to process data with an isotropic resolution 
other than 1mm^3 with FreeSurfer v5.1 and above here:
https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon

For v5.3 the pipeline should be slightly adapted, however, can easily be done. 
If you need assistance, just let me know. In the upcoming release of v6 this 
workaround will not necessary anymore.

Best,
Falk

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Trisanna 
Sprung-Much
Gesendet: Mittwoch, 25. Mai 2016 17:35
An: Freesurfer support list
Betreff: [Freesurfer] recon-all on 0.5mm scan?

Hi Freesurfer
I would like to know if it is possible to create surfaces from a scan that is 
0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is 0.5mm 
cubed and it crashed quite quickly afterwards. I wonder if this has to do with 
the fact that Freesurfer tried to conform it to 1mm isotropic?
When I ran recon-all on the 1mm atlas it created some nice surfaces.
Let me know if you would like the .log as I cannot seem to make much sense of 
it.
best wishes
Trisanna
--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


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[Freesurfer] Rat model in FreeSurfer

[Melanie Ganz]

Hi,

one of our lab mates who works with small animal models would also like 
to try FreeSurfer. I know from the mail archive that people have used it 
like this before.


Could any people that have used it on rats please give some info on what 
they have tried?


Cheers,
Melanie

--
Melanie Ganz-Benjaminsen, MSc, Ph.D.
Neurobiology Research Unit
University of Copenhagen
Rigshospitalet
Rockefeller Center
Juliane Maries Vej 28/30, 3.
DK-2100 Copenhagen
Denmark

phone:  +45 3545 6718
e-mail: melanie.g...@nru.dk
web: http://melanie.clausundmelanie.de/

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