Re: [Freesurfer] total brain volume or intra crainal volume as estimated for total brain volume

[Knut J Bjuland]

Hi Doug

I have run recon-all -segstats -s subject on all my subjects, but I can not see 
total brain volume label. 
Should I use intra cranial volume?


Knut J

> Date: Mon, 4 Jun 2012 10:09:16 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] total brain volume or intra crainal volume as 
> estimated for total brain volume
> 
> Hi Knut, you can copy the following file into 
> $FREESURFER_HOME/bin/mri_segstats
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
> (assuming you're using linux)
> The run
> recon-all -segstats -s subject
> This will create a new aseg.stats file with total brain volume based on 
> adding up the values in the segmentation.
> doug
> 
> 
> 
> On 06/04/2012 05:20 AM, Knut J Bjuland wrote:
> > Hello,
> >
> > We would like to  calculate a Total Brain Volume based on data in 
> > aseg.stat generated from version 5.1.0. Can I use intra crainal volume 
> > as estimated for total brain volume? Or should I just add total grey 
> > volume with subcortical grey volume with total white matter volume?
> >
> > Thanks,
> > Knut Jørgen
> >
> >
> > ___
> > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
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> 
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[Freesurfer] correction for multiple comparisons

[Marie Schneider]

Dear FreeSurfer experts,

I have some questions about corrections for multiple comparisons in
FreeSurfer. I have two samples, one consisting of two groups and one
consisting of three groups.

I do the comparison with the sample of two groups in qdec. Correcting for
multiple comparisons, I get a significant result using FDR, but no
significant result using Monte Carlo simulation. How can that be?

I analyze the sample with the three groups by mri_glmfit. In your tutorial,
I only found how to correct for multiple comparisons with the Monte Carlo
simulation using the command line, but not how to correct with FDR using
the command line. Is there a possibility to do this? If not, how many
iterations are usual to use within the Monte Carlo simulation?

Any help is appreciated.

Thank you very much,

Marie
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[Freesurfer] p-value of clusters

[Richter, Julia]

Dear all,

I am running a qdec analysis. When I press "Find clusters and Goto Max", all 
values of the significant clusters after FDR correcting appear except for the p 
values of the clusters. Any idea why this is happening and what I can do?

Best, Julia

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[Freesurfer] Questions regarding statistical analysis

[KimMJ]

Dear FS experts
I'm completely new to the world of freesurfer and apologize my silly queries.
I'm trying to compare GM volume, cortical thickness, and mean curvature of 34 
automatically parcellated cortical structures (data from 'aparcstats2table' 
command) between control and patient groups (N=32 for each) using SPSS.
Here are my questions.1) It seems reasonable that statistical model of 
between-group comparison of each cortical GM volume should include age, sex, 
and intracranial (or cortical total GM volume) as covariates.But, should I also 
include intracranial volume (or cortical GMV) as a covariate in cases of 
cortical thickness and mean curvature ?? (Please note what I'm trying to do is 
NOT whole brain image analysis BUT MANCOVA using SPSS)When searching for the 
published articles containing cortical thickness analysis identical to what I'm 
doing, I found some use such a covariate, but some did not.Please let me know 
the better method.
2) My second questions is not directly related to FreeSurfer.From the 
above-mentioned analysis (MANCOVA: 2 groups, 34 dependent variables, 2 or 3 
covariates), should I correct for multiple comparison problem using Bonferroni 
corrected P < 0.05/34=0.0014) or FDR-corrected P < 0.05 ??
Once again, apologies for my basic questions.Any comment would be greatly 
appreciated.
Thank you in advance for your kind help.
M. KimSouth Korea





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[Freesurfer] repost - large-scale reconstruction errors

[Nicole Senecal]

Hi,

In reconstructing some normal adult MPRAGEs, I've had a couple of different
fairly large errors that I haven't been able to fix:
(1) In a handful of subjects, more than half of the brain is lost, I think
during the skullstripping step (ie, isn't present on the white matter or
brainmask volumes later). This seems to be primarily on scans from a 3T
Siemens with a 32channel head coil. I have tried adding control points, but
this doesn't help.
(2) In another handful of subjects, a large portion of the cerebellum is
designated as cortex, and is labeled on the aseg maps.

Any suggestions on how to fix these two types of problems?

thanks,
Nicole


-- 
Nicole Senecal
Neuroscience Graduate Group
Kable Lab
3720 Walnut St., Room C37
Philadelphia, PA  19104
Lab phone:  215-746-4371
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Re: [Freesurfer] 回复: Re: /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory

[Xiangzhen Kong]

Thanks for your rapid reply .

best!




Xiangzhen Kong

发件人： Anastasia Yendiki
发送时间： 2012-06-07 23:19
收件人： Xiangzhen Kong
抄送： freesurfer
主题： Re: [Freesurfer] 回复: Re: /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such 
file or directory

Hi Xiangzhen - Currently mri_convert does not support extracting gradients 
and b-values from dicom files. If you can get the gradients and b-values 
from the dicom header yourself, that's great. Save them in text files and 
enter the path in your dmrirc file.

a.y

On Thu, 7 Jun 2012, Xiangzhen Kong wrote:

> Thank you very much, Anastasia.
> I have checked the related mails in the list and found not me came across
> this problem.
> As you said, I know how I can run my data.
> But I have a question. Why would we make trac-all compatible to other
> scanner or acquisitions, since we can get bvecs and bval from the DICOM
> header?
>  
> thank in advance.
>  
>  
> 
> 
> Xiangzhen Kong
>  
> From: Anastasia Yendiki
> Date: 2012-02-04 00:52
> To: Xiangzhen Kong
> CC: freesurfer
> Subject: Re: [Freesurfer] /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such
> file or directory
>  
> Unless your dicoms came from the same acquisition as the default 
> MGH/Siemens one, you'll have to set bvecfile and bvalfile and provide 
> those files yourself.
>  
> On Fri, 3 Feb 2012, Xiangzhen Kong wrote:
>  
> > Hi all
> > Now I am learning the trac-all using with DICOM data, but came across a
> > problem.
> > +++
> > mv?f?xxx/dmri/dwi_orig_flip.mghdti.bvecs?/dmri/bvecs
> > mv:燾annot爏tat燻/xxx/dmri/dwi_orig_flip.mghdti.bvecs':燦o爏uch爁ile爋r
?? ??ir
> > ectory
> > +++
> > I check the dir /xxx/dmri/ and there are only two files
> > 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz'?and a dir 'xfms'.
> > Does trac-all extract bvals/bvecs automatically when start with DICOM dat
> a?
> > My data is from a siemens scanner.
> > ?
> > Thanks!
> > ?
> > Xiangzhen
> > ?
> > 2012-02-03
> > 
> > _
> ___
> > Xiangzhen Kong
> > 
> >
>  
>  
> The information in this e-mail is intended only for the person to whom it i
> s
> addressed. If you believe this e-mail was sent to you in error and the e-ma
> il
> contains patient information, please contact the Partners Compliance HelpLi
> ne at
> http://www.partners.org/complianceline . If the e-mail was sent to you in e
> rror
> but does not contain patient information, please contact the sender and pro
> perly
> dispose of the e-mail.
>  
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Re: [Freesurfer] Creating a label from an .mgh file

[Ilia]

Thanks for the reply.

Couple of follow up questions.

(1) Which "ID" should be used when creating the mask?
The "mc-z.abs.th23.sig.cluster.mgh" file contains clusters labeled based 
on z values (i.e., non-integers such as -3.698970, +2.130768, etc).
Is it possible to divide the *.mgh file by itself to produce a file with 
1's where clusters exist?
That approach would work in FSL, but I am not quite sure what tools 
exist in FS or how to use them.

(2) How would one visualize the resulting label file in tksurfer? Using 
"File-->Label-->Load Label" results in yellow specks showing up on the 
brain surface, but the spatial locations aren't correct (they don't 
correspond to where clusters exist on the original volume).

Any help would be appreciated.
> Message: 13
> Date: Wed, 06 Jun 2012 18:04:56 -0400
> From: Douglas Greve 
> Subject: Re: [Freesurfer] Creating a label from an .mgh file
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <4fcfd408.6050...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> you can use mri_cor2label, eg, for cluster #2, something like
>
> mri_cor2label --id 2 --i cluster.mgh --o cluster2.label
>
> doug
>
> On 6/6/12 4:22 PM, Ilia wrote:
>   
>> Hello,
>>
>> How would one create a label (to be used as an input for
>> "mris_anatomical_stats") based on a a statistical map generated by qdec
>> (for example, the result of a Monte Carlo simulation such as
>> "mc-z.abs.th23.sig.cluster.mgh").
>>
>> The goal is to obtain average cortical thickness for regions where qdec
>> detected significance.
>>
>> Thank you!!
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> 
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Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

[Douglas N Greve]

I've put a new version of mri_label2vol at that ftp site. When you run 
it, add "--offset 1". This will change the segmentations IDs to go from 
1-162 instead of 0-161.
doug

On 06/08/2012 11:30 AM, Leon wrote:
> Hi, Douglas
>
> I checked the data this morning and confirmed that the missing ROI in 
> the volume space is vertex_0 (see attached). Totally there are 162 
> entries in the annotation file, but only 161 left in the volume file 
> after transferring the annotation file to the volume using 
> mri_label2vol and the intensity value ranges from 1 to 161.
>
> Thanks
>
> Leon
>
> PS: I am sending the message again because I was told that the image 
> for the previous mail is too big.
>
> *From:* Leon 
> *To:* Douglas N Greve 
> *Cc:* FreeSurfer 
> *Sent:* Thursday, June 7, 2012 10:52 PM
> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to 
> transfer ic2.tri
>
> Hi, Douglas
>
> Thank you very much for taking care of it. The ROIs ending with 2 and 
> 5s have been correctly labeled and have volumes now after running the 
> fixed version of mris_make_face_parcellation.  However, there is still 
> one ROI missing in the volume data that is located at the top of the 
> postcentral gyrus after the annotation file was transferred from the 
> subject's surface to the volume using mri_label2vol. I checked the 
> index of the ROI yesterday (I am at home now and do not have access to 
> the data) and I remember the index of the missing ROI is  vertex_0 and 
> the location of the ROI is identical as the one in the picture I 
> attached in the previous email. Do you think it might be because the 
> mri_label2vol overlooks the index of 0, as the intensity value in the 
> volumes starts with 1?
>
> I would appreciate your help on this.
>
> Leon
>
> *From:* Douglas N Greve 
> *To:* Leon 
> *Cc:* FreeSurfer 
> *Sent:* Thursday, June 7, 2012 2:03 PM
> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to 
> transfer ic2.tri
>
> Hi Leon, I found the problem. mris_make_face_parcellation was actually
> merging several units together. You can get a fixed version from here:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_make_face_parcellation.linux
> Let me know how it goes
> doug
>
> On 06/04/2012 02:44 PM, Leon wrote:
> > Hi, Douglas
> > I have uploaded the file to the system.
> > Also, my new results showed that  when  ic3.tri (instead of ic2.tri)
> > is used as the input, one ROI at the similar location is also missing.
> > Hope it will help you diagnose.
> >
> > Thanks
> > Leon
> >
> > *From:* Douglas N Greve  >
> > *To:* Leon mailto:leonad...@yahoo.com>>
> > *Cc:* FreeSurfer  >
> > *Sent:* Monday, June 4, 2012 1:00 PM
> > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
> > transfer ic2.tri
> >
> > Can you upload the subject to our file drop system?
> >
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
> > 
> >
> >
> >
> >
> > On 06/04/2012 12:24 PM, Leon wrote:
> > > Hi, Douglas
> > >
> > > Thank you very much for the updated one. I tested the new codes and
> > > the problem is still there. The ID for the original version that
> > > generates a mask with one missing ROI is:
> > >
> > > $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
> > >
> > > I remember this is a version I downloaded from a link in FS archive.
> > >
> > > The ID for the one you sent to me is:
> > >
> > > $Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $
> > >
> > > They look almost identical. Do you have any ideas what else may cause
> > > this issue and possible workaround?
> > >
> > > Thank you
> > >
> > > Leon
> > >
> > >
> > > *From:* Douglas Greve  
> > >>
> > > *To:* freesurfer@nmr.mgh.harvard.edu 
> 
> >  >
> > > *Sent:* Friday, June 1, 2012 11:29 PM
> > > *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
> > > transfer ic2.tri
> > >
> > >
> > > What version are you using? I fix a problem last Sept that might be
> > > like this. I've put a new version of mri_label2vol here:
> > >
> > 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
> > > Try this and let me know if it works.
> > > doug
> > >
> > >
> > > On 6/1/12 10:46 PM, Leon wrote:
> > >> Hi, Bruce
> > >> Here are my two command lines
> > >> For transferring the annot from the source template to the target
> > >> subject:
> > >>
> > >> /home/freesurfer/bin/mri_surf2surf --srcsubject ${srcsubject}
> > >> --sval-annot rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval
> > >> src_2_trg.annot --hemi rh --surfreg sphere.reg0

Re: [Freesurfer] Using an ROI and not correcting/"fixing" the rest of the image

[Kairys, Anson]

Thanks for the quick response! I will begin basic processing and will surely 
have questions about how the sphere.reg file is used/how it applies.

Thanks again 

Anson
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Thursday, June 07, 2012 12:40 PM
To: Kairys, Anson
Cc: 'freesurfer@nmr.mgh.harvard.edu'
Subject: Re: [Freesurfer] Using an ROI and not correcting/"fixing" the rest of 
the image

Hi Anson

yes, that's ok as long as you make sure that the registration
(sphere.reg) is ok for group results.

cheers
Bruce
On Thu, 7 Jun 2012, Kairys, Anson
wrote:

> 
> Hi,
> 
>  
> 
> I am planning on looking at a specific region of interest, and I am 
> wondering it is possible to only ?quality check? this region and leave 
> the rest of the brain as is.
> 
>  
> 
> Meaning, can I save the time of going through every slice and 
> re-assigning voxels for the entire brain and just focus on making sure 
> the estimation of WM etc. is correct in my ROI?
> 
>  
> 
> Thanks a lot for any help you can provide.
> 
>  
> 
> Best wishes
> 
>  
> 
> Anson
> 
> **
> Electronic Mail is not secure, may not be read every day, and should 
> not be used for urgent or sensitive issues
>


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Re: [Freesurfer] Creating a label from an .mgh file

[Douglas N Greve]

Sorry, use the "ocn" file, not the cluster file. This should have 
integer values, one for each cluster.
doug

On 06/08/2012 01:04 PM, Ilia wrote:
> Thanks for the reply.
>
> Couple of follow up questions.
>
> (1) Which "ID" should be used when creating the mask?
> The "mc-z.abs.th23.sig.cluster.mgh" file contains clusters labeled based
> on z values (i.e., non-integers such as -3.698970, +2.130768, etc).
> Is it possible to divide the *.mgh file by itself to produce a file with
> 1's where clusters exist?
> That approach would work in FSL, but I am not quite sure what tools
> exist in FS or how to use them.
>
> (2) How would one visualize the resulting label file in tksurfer? Using
> "File-->Label-->Load Label" results in yellow specks showing up on the
> brain surface, but the spatial locations aren't correct (they don't
> correspond to where clusters exist on the original volume).
>
> Any help would be appreciated.
>> Message: 13
>> Date: Wed, 06 Jun 2012 18:04:56 -0400
>> From: Douglas Greve
>> Subject: Re: [Freesurfer] Creating a label from an .mgh file
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:<4fcfd408.6050...@nmr.mgh.harvard.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> you can use mri_cor2label, eg, for cluster #2, something like
>>
>> mri_cor2label --id 2 --i cluster.mgh --o cluster2.label
>>
>> doug
>>
>> On 6/6/12 4:22 PM, Ilia wrote:
>>
>>> Hello,
>>>
>>> How would one create a label (to be used as an input for
>>> "mris_anatomical_stats") based on a a statistical map generated by qdec
>>> (for example, the result of a Monte Carlo simulation such as
>>> "mc-z.abs.th23.sig.cluster.mgh").
>>>
>>> The goal is to obtain average cortical thickness for regions where qdec
>>> detected significance.
>>>
>>> Thank you!!
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
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>
>

-- 
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Mris_anatomical_stats: smoothing does not work with surface area maps

[Douglas N Greve]

Hi Juegen, there will be a file called something like 
cache.th20.abs.y.ocn.dat in the glm output directory. This will be a 
text file with number of columns equal to the number of significant 
clusters (after correction) and number of rows equal to the number of 
subjects. The value will be the average over that cluster for that 
subject. Is this what you want? This will correspond exactly with the 
map-based data, which you'll never be able to do by mapping the clusters 
back to each individual subject because of resampling issues.
doug

On 06/08/2012 02:37 AM, Jürgen Hänggi wrote:
> Hi Doug
>
> I correlated a behavioural measure with cortical thickness and surface area
> using mri_preroc, mri_surf2surf and mri_glmfit. Now I would like to extract
> the individual values of the clusters that correlated with the behavioural
> measure.
> Because the individual values should be comparable with the results of the
> group, I have to smooth them too.
>
> When using --sval lh.area, the following error occurred:
>
> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
> foreach s ( MOREA_* )
> foreach? mri_surf2surf --hemi lh --s $s --sval lh.area --fwhm 15 --tval
> lh.area.15.mgh --cortex
> foreach? end
> ERROR: could not determine type of lh.area
> ...
> ...
> ...
> ERROR: could not determine type of lh.area
> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
>
> Thanks
> Cheers
> Jürgen
>
> On [DATE], "Douglas N Greve"<[ADDRESS]>  wrote:
>
>> Use "--sval lh.area". Also, why do you want to smooth it before
>> averaging over the ROI?
>> doug
>>
>> On 06/07/2012 01:29 AM, Jürgen Hänggi wrote:
>>> Hi Doug
>>>
>>> This is my command line:
>>>
>>> mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area
>>> -nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
>>>
>>> In the past, you recommended smoothing the data with mri_surf2surf instead
>>> of with mris_anatomical_stats.
>>>
>>> For that purpose, I run the following command:
>>>
>>> mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval
>>> lh.area.15.mgh --cortex
>>>
>>> But the following error occurred:
>>>
>>> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
>>> foreach s ( MOREA_* )
>>> foreach? mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval
>>> lh.area.15.mgh --cortex
>>> foreach? end
>>> srcsubject = MOREA_KG002
>>> srcval = (null)
>>> srctype=
>>> trgsubject = MOREA_KG002
>>> trgval = lh.area.15.mgh
>>> trgtype=
>>> srcsurfreg = sphere.reg
>>> trgsurfreg = sphere.reg
>>> srchemi= lh
>>> trghemi= lh
>>> frame  = 0
>>> fwhm-in= 0
>>> fwhm-out   = 15
>>> label-src  = (null)
>>> label-trg  = lh.cortex.label
>>> OKToRevFaceOrder  = 1
>>> Reading source surface reg
>>> /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg
>>> Loading source data
>>> Reading surface file
>>> /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area
>>> nquads=9895939,  nvertices=399
>>> ERROR: MRISread: file
>>> '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more
>>> faces than vertices!
>>> Probably trying to use a scalar data file as a surface!
>>>
>>> Thanks for help in advance
>>> Cheers
>>> Jürgen
>>>
>>> On [DATE], "Douglas Greve"<[ADDRESS]>   wrote:
>>>
 what is your command line?
 doug

 On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
> Dear FS experts
>
> I have done group comparisons wrt thickness and surface area. The
> found clusters were written out as annotations, transformed into each
> individual space, and then the corresponding values were extracted.
>
> When using mris_anatomical_stats, values are different for thickness maps
> depending whether I used the --nsmooth 15 option or not. So good
> so far.
>
> However, when using the same command (see below) for ?h.area files,
> extracted values are the same whether or not I used the --nsmooth option.
>
> It seems that the --nsmooth option in mris_anatomical_stats does not
> affect (smooth) the surface area maps.
>
> Is there any solution to also smooth surface area maps with
> mris_anatomical_stats?
>
> I use the Mac FS 5.1.0 version
>
> Thanks in advance
> Best regards
> Jürgen Hänggi
>
>
>
> ---
> -
> Jürgen Hänggi, Ph.D.
> Division Neuropsychology
> Institute of Psychology
> University of Zurich
> Binzmuehlestrasse 14, PO Box 25
> 8050 Zurich, Switzerland
> 0041 44 635 73 97 (phone office)
> 0041 76 445 86 84 (phone mobile)
> 0041 44 635 74 09 (fax office)
> BIN 4.D.04 (office room number)
> j.haenggi[at]psychologie.uzh.ch (email)
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> http://www.juergenhaenggi.ch (private website)
>
> This e-mail (and any attachment/s) 

[Freesurfer] qdec.table.dat

[Kushal Kapse]

hi doug,

i am loading 917 subjects in qdec.i already made qdec.table.dat which 
consist the list of subjid, age, gender, lh & rh thickness..


for some reason, it is only displaying the first subject.others are not 
been detected by qdec.
i also looked into tutorial and compared the tutorial qdec.table.dat file with 
the one i madeboth r identical and look good..$SUBJECTS_DIR already has 
glm, qdec and fsaverage foldersStill; it displaying only one subject.

any idea why is it doing as i tried several ways to find the fix but hasnt been 
successful yetplease let me know


thanks
kk

- Original Message -
From: "Douglas N Greve" 
To: "Jürgen Hänggi" 
Cc: "Freesurfer Mailinglist" 
Sent: Friday, June 8, 2012 4:17:02 PM
Subject: Re: [Freesurfer] Mris_anatomical_stats: smoothing does not work with 
surface area maps

Hi Juegen, there will be a file called something like 
cache.th20.abs.y.ocn.dat in the glm output directory. This will be a 
text file with number of columns equal to the number of significant 
clusters (after correction) and number of rows equal to the number of 
subjects. The value will be the average over that cluster for that 
subject. Is this what you want? This will correspond exactly with the 
map-based data, which you'll never be able to do by mapping the clusters 
back to each individual subject because of resampling issues.
doug

On 06/08/2012 02:37 AM, Jürgen Hänggi wrote:
> Hi Doug
>
> I correlated a behavioural measure with cortical thickness and surface area
> using mri_preroc, mri_surf2surf and mri_glmfit. Now I would like to extract
> the individual values of the clusters that correlated with the behavioural
> measure.
> Because the individual values should be comparable with the results of the
> group, I have to smooth them too.
>
> When using --sval lh.area, the following error occurred:
>
> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
> foreach s ( MOREA_* )
> foreach? mri_surf2surf --hemi lh --s $s --sval lh.area --fwhm 15 --tval
> lh.area.15.mgh --cortex
> foreach? end
> ERROR: could not determine type of lh.area
> ...
> ...
> ...
> ERROR: could not determine type of lh.area
> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
>
> Thanks
> Cheers
> Jürgen
>
> On [DATE], "Douglas N Greve"<[ADDRESS]>  wrote:
>
>> Use "--sval lh.area". Also, why do you want to smooth it before
>> averaging over the ROI?
>> doug
>>
>> On 06/07/2012 01:29 AM, Jürgen Hänggi wrote:
>>> Hi Doug
>>>
>>> This is my command line:
>>>
>>> mris_anatomical_stats -a area_left_significant_labels.annot -t lh.area
>>> -nsmooth 15 -f $s/stats/lh.aparc.a2005s.stats $s lh
>>>
>>> In the past, you recommended smoothing the data with mri_surf2surf instead
>>> of with mris_anatomical_stats.
>>>
>>> For that purpose, I run the following command:
>>>
>>> mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval
>>> lh.area.15.mgh --cortex
>>>
>>> But the following error occurred:
>>>
>>> [Juergen-Haenggis-Mac-Pro:/Applications/freesurfer/subjects] juergenhaenggi%
>>> foreach s ( MOREA_* )
>>> foreach? mri_surf2surf --hemi lh --s $s --sval-area area --fwhm 15 --tval
>>> lh.area.15.mgh --cortex
>>> foreach? end
>>> srcsubject = MOREA_KG002
>>> srcval = (null)
>>> srctype=
>>> trgsubject = MOREA_KG002
>>> trgval = lh.area.15.mgh
>>> trgtype=
>>> srcsurfreg = sphere.reg
>>> trgsurfreg = sphere.reg
>>> srchemi= lh
>>> trghemi= lh
>>> frame  = 0
>>> fwhm-in= 0
>>> fwhm-out   = 15
>>> label-src  = (null)
>>> label-trg  = lh.cortex.label
>>> OKToRevFaceOrder  = 1
>>> Reading source surface reg
>>> /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.sphere.reg
>>> Loading source data
>>> Reading surface file
>>> /Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area
>>> nquads=9895939,  nvertices=399
>>> ERROR: MRISread: file
>>> '/Applications/freesurfer/subjects/MOREA_KG002/surf/lh.area' has many more
>>> faces than vertices!
>>> Probably trying to use a scalar data file as a surface!
>>>
>>> Thanks for help in advance
>>> Cheers
>>> Jürgen
>>>
>>> On [DATE], "Douglas Greve"<[ADDRESS]>   wrote:
>>>
 what is your command line?
 doug

 On 6/6/12 5:25 AM, Jürgen Hänggi wrote:
> Dear FS experts
>
> I have done group comparisons wrt thickness and surface area. The
> found clusters were written out as annotations, transformed into each
> individual space, and then the corresponding values were extracted.
>
> When using mris_anatomical_stats, values are different for thickness maps
> depending whether I used the --nsmooth 15 option or not. So good
> so far.
>
> However, when using the same command (see below) for ?h.area files,
> extracted values are the same whether or not I used the --nsmooth option.
>
> It seems that the --nsmooth option in mris_anatomical_stats does not
> affect (smooth) the surface

Re: [Freesurfer] correction for multiple comparisons

[Douglas N Greve]

they are two different correction schemes. If they gave the same answer, 
then it would not make sense to have both. the monte carlo tries to 
compute the probability of a cluster of the given size under the null 
hypothesis. FDR controls for the number of false positives relative to 
the total number of positives under the assumption that if any 5% of 
your positives are false, then you would not change your conclusion.

For monte carlo, we generally use 1 iterations. If you are using the 
whole hemisphere, then you can used the cached tables. See the 
"command-line" tutorial.

doug

On 06/08/2012 08:03 AM, Marie Schneider wrote:
> Dear FreeSurfer experts,
>
> I have some questions about corrections for multiple comparisons in 
> FreeSurfer. I have two samples, one consisting of two groups and one 
> consisting of three groups.
>
> I do the comparison with the sample of two groups in qdec. Correcting 
> for multiple comparisons, I get a significant result using FDR, but no 
> significant result using Monte Carlo simulation. How can that be?
>
> I analyze the sample with the three groups by mri_glmfit. In your 
> tutorial, I only found how to correct for multiple comparisons with 
> the Monte Carlo simulation using the command line, but not how to 
> correct with FDR using the command line. Is there a possibility to do 
> this? If not, how many iterations are usual to use within the Monte 
> Carlo simulation?
>
> Any help is appreciated.
>
> Thank you very much,
>
> Marie
>
>
> ___
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] repost - large-scale reconstruction errors

[Bruce Fischl]

Hi Nicole
If you upload some examples we will take a look. What version as you running? 
Have you checked the accuracy of the talairach.xfm?

Cheers
Bruce



On Jun 8, 2012, at 11:19 AM, Nicole Senecal  wrote:

> Hi,
> 
> In reconstructing some normal adult MPRAGEs, I've had a couple of different 
> fairly large errors that I haven't been able to fix:
> (1) In a handful of subjects, more than half of the brain is lost, I think 
> during the skullstripping step (ie, isn't present on the white matter or 
> brainmask volumes later). This seems to be primarily on scans from a 3T 
> Siemens with a 32channel head coil. I have tried adding control points, but 
> this doesn't help. 
> (2) In another handful of subjects, a large portion of the cerebellum is 
> designated as cortex, and is labeled on the aseg maps. 
> 
> Any suggestions on how to fix these two types of problems? 
> 
> thanks,
> Nicole
> 
> 
> -- 
> Nicole Senecal
> Neuroscience Graduate Group
> Kable Lab
> 3720 Walnut St., Room C37
> Philadelphia, PA  19104
> Lab phone:  215-746-4371
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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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.