Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[Douglas Greve]

don't use --init-rr ( you don't need to spec an init in version 6)


On 4/10/18 9:48 PM, srishti goel wrote:
When I run bbregister, it gives me an error. Attached is the 
register.dat.log file for it.

Error:

reading source './tmp.bbregister.91068/template.nii'...

mri_robust_register.bin: only pass single frame MRI source 
./tmp.bbregister.91068/template.nii.



No such file or directory


Any help is greatly appreciated!


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12


On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve 
> wrote:


They are not in registration. Try running bbregister to create a
registration file (lta), then pass the lta to tkregisterfv instead
of --regheader


On 4/9/18 11:49 PM, Bruce Fischl wrote:

How did you generate the registration? And give us the details of
what you are trying to register
Cheers
Bruce

On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtig...@gmail.com
> wrote:


Hi Bruce,

Thanks so much for pointing that out, I totally missed that part.

Also, the registration definitely isn't appropriate.
Could someone please guide me how to correct this problem. I
have attached a screenshot of how it looks like currently.




Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12


On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl
>
wrote:

Hi Srishti

the directory you are in doesn't matter. YOu either need to
set SUBJECTS_DIR in the environment, or use --sd
 to specify the
directory that contains your subjects. I think you can also
give it the full path to a target volume if you want, but
maybe Doug can comment as he knows this stuff better than I do

cheers
Bruce



 On Sun, 8 Apr 2018, srishti goel wrote:

When I type this command:tkregisterfv --mov
negative_allsocial_proportion.nii --regheader --s
mni152_subject --surfs --reg reg.deleteme.dat

It gives me the error: cannot find mni152_subject.
Although I clearly checked that the directory from which
I am submitting this command has the
mni152_subject directory within which there are all the
other required directories such as: mri,
stats, surf, scripts, etc.

I am unsure what is happening here.


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu

skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve
>
wrote:
      Those commands look ok. My suspicion goes to the
use of --regheader. See
      whether the registration is ok with

      tkregisterfv --mov
negative_allsocial_proportion.nii --regheader --s
      mni152_subject --surfs --reg reg.deleteme.dat


      On 04/05/2018 08:34 AM, srishti goel wrote:
      > Hi,
      >
      > I am trying to compare my volume maps
      > (negative_allsocial_proportion.nii) to someone
else's
      > (SN_like_cortical_lh.nii.gz) who have it on a
surface
      > (mni152_subject). So I used the steps for
mri_vol2surf command as
      > follows:
      >
      > Commands:
      > mri_vol2surf --src
negative_allsocial_proportion.nii --regheader
      > mni152_subject --hemi lh --o
./neg_allsocial_lh.nii --projfrac 0.5
      > Then to view it:
      > tksurfer mni152_subject lh inflated -overlay
./neg_allsocial_lh.nii
      > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
      >
      > Everything ran fine and we didn't get any error
but then while viewing
      > the files we could not see our map
(neg_allsocail_lh.nii) on the
      > surface. This file seemed to work fine as it is
not an empty file when
      > I checked the 

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[srishti goel]

When I run bbregister, it gives me an error. Attached is the
register.dat.log file for it.
Error:

reading source './tmp.bbregister.91068/template.nii'...

mri_robust_register.bin: only pass single frame MRI source
./tmp.bbregister.91068/template.nii.


No such file or directory


Any help is greatly appreciated!

Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu
skype: srishti.goel12


On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve 
wrote:

> They are not in registration. Try running bbregister to create a
> registration file (lta), then pass the lta to tkregisterfv instead of
> --regheader
>
> On 4/9/18 11:49 PM, Bruce Fischl wrote:
>
> How did you generate the registration? And give us the details of what you
> are trying to register
> Cheers
> Bruce
>
> On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtig...@gmail.com> wrote:
>
> Hi Bruce,
>
> Thanks so much for pointing that out, I totally missed that part.
>
> Also, the registration definitely isn't appropriate.
> Could someone please guide me how to correct this problem. I have attached
> a screenshot of how it looks like currently.
>
>
> 
>
> Best,
> Srishti
> Social/Clinical Research Specialist
> Child Imaging Research and Life Experiences Lab
> University of North Carolina at Chapel Hill
> email (W): srish...@email.unc.edu
> skype: srishti.goel12
>
>
> On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl 
> wrote:
>
>> Hi Srishti
>>
>> the directory you are in doesn't matter. YOu either need to set
>> SUBJECTS_DIR in the environment, or use --sd  to specify the
>> directory that contains your subjects. I think you can also give it the
>> full path to a target volume if you want, but maybe Doug can comment as he
>> knows this stuff better than I do
>>
>> cheers
>> Bruce
>>
>>
>>
>>  On Sun, 8 Apr 2018, srishti goel wrote:
>>
>> When I type this command:tkregisterfv --mov negative_allsocial_proportion.nii
>>> --regheader --s
>>> mni152_subject --surfs --reg reg.deleteme.dat
>>>
>>> It gives me the error: cannot find mni152_subject.
>>> Although I clearly checked that the directory from which I am submitting
>>> this command has the
>>> mni152_subject directory within which there are all the other required
>>> directories such as: mri,
>>> stats, surf, scripts, etc.
>>>
>>> I am unsure what is happening here.
>>>
>>>
>>> Best,
>>> Srishti
>>> Social/Clinical Research Specialist
>>> Child Imaging Research and Life Experiences Lab
>>> University of North Carolina at Chapel Hill
>>> email (W): srish...@email.unc.edu
>>> skype: srishti.goel12
>>>
>>>
>>> On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve <
>>> dgr...@mgh.harvard.edu> wrote:
>>>   Those commands look ok. My suspicion goes to the use of
>>> --regheader. See
>>>   whether the registration is ok with
>>>
>>>   tkregisterfv --mov negative_allsocial_proportion.nii --regheader
>>> --s
>>>   mni152_subject --surfs --reg reg.deleteme.dat
>>>
>>>
>>>   On 04/05/2018 08:34 AM, srishti goel wrote:
>>>   > Hi,
>>>   >
>>>   > I am trying to compare my volume maps
>>>   > (negative_allsocial_proportion.nii) to someone else's
>>>   > (SN_like_cortical_lh.nii.gz) who have it on a surface
>>>   > (mni152_subject). So I used the steps for mri_vol2surf command as
>>>   > follows:
>>>   >
>>>   > Commands:
>>>   > mri_vol2surf --src negative_allsocial_proportion.nii --regheader
>>>   > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii --projfrac
>>> 0.5
>>>   > Then to view it:
>>>   > tksurfer mni152_subject lh inflated -overlay
>>> ./neg_allsocial_lh.nii
>>>   > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
>>>   >
>>>   > Everything ran fine and we didn't get any error but then while
>>> viewing
>>>   > the files we could not see our map (neg_allsocail_lh.nii) on the
>>>   > surface. This file seemed to work fine as it is not an empty
>>> file when
>>>   > I checked the file size. However, when we view it using tksurfer
>>> it
>>>   > does not show up as a highlighted portion on the surface. The
>>>   > SN_like_cortical_lh.nii.gz file shows up just fine.
>>>   >
>>>   > Could someone please help me figure out what might have gone
>>> wrong here.
>>>   >
>>>   > Thanks so much!
>>>   >
>>>   >
>>>   >
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>> ___
>>> 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 

Re: [Freesurfer] newbie trac-all -bedp question

[Yendiki, Anastasia]

Hi Don - If the output files described here show up in the end, all is well:


https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#BEDPOSTX


Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Krieger, Donald N. 

Sent: Tuesday, April 10, 2018 4:52:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Great – thanks.

It’s running.

I see several warnings which I presume can be ignored:

hostname: Name or service not known



Best - Don





From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer 
Subject: Re: [Freesurfer] newbie trac-all -bedp question



Hi Don - See: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html



Best,

a.y



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 on behalf of Krieger, Donald N. >
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question



I am getting the following output with error on this command:



trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23



INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131: 
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected



I apologize for not finding the answer in the list archive.

It's probably there.



I'm running under ubuntu 14.04.



bedpostx_mgh is a shell script which calls for /bin/sh.

On my machine, that is a symlink to /bin/bash

If I change it to be explicitly /bin/bash, it runs a bit further.

Here is the full output:



INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects

Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0

WARN: Running bedbostx locally - this might take a while

WARN: It is recommended to run this step on a cluster

bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

subjectdir is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri

Making bedpostx directory structure

Queuing preprocessing stages

/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")

Queuing parallel processing stage

0 slices processed

/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")

Queuing post processing stage

/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")

/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: line 439: 26461 Terminated  
${subjdir}.bedpostX/monitor





Thanks - Don


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Re: [Freesurfer] how to control for head size differences when measuring global atrophy?

[Douglas N. Greve]

As far a I know, thickness does not vary with head size, so we don't 
traditionally make a correction


On 04/10/2018 01:52 PM, Maria Gloria Rossetti wrote:
> Thanks for getting back to me.
> My hp is the same as for the volumetric analysis. I want to measure 
> thickness differences between patients and controls while controlling 
> for major confounders (head size included). However, since 
> thickness doesn't scale with eTIV as much as volume how can I control 
> for head size variability? What would you suggest me to do? I am not 
> that familiar with thickness analysis and I would not add unnecessary 
> noise.
>
> Best,
> Gloria
>
> (n.b. in my sample,   eTIV is significantly different between 
> groups) Best,
>
>
> 
> *Da: *"Douglas Greve" 
> *A: *"freesurfer" 
> *Inviato: *Martedì, 10 aprile 2018 16:24:42
> *Oggetto: *Re: [Freesurfer] how to control for head size differences 
> when measuring global atrophy?
>
> I would probably correct total GM, total WM, and total ventricular CSF 
> by head size. It is not surprising that they covary a lot (as you 
> point out). But what you want is what is left over after you remove 
> the effect. You can also divide by the eTIV rather than regressing it 
> out, but the results will be similar.
>
> As for thickness, many people regress out the mean thickness, but this 
> changes the hypothesis that you are testing (and so the interpretation 
> of the results). As such, this is a question that you will have to 
> answer yourself.
>
>
> On 4/9/18 10:11 AM, Maria Gloria Rossetti wrote:
>
> Dear freesurfers
>
> my study aims to measure volumetric differences between patients X
> and controls. As dependent variables, I have (i) a-priori ROIs and
> (ii) global brain measures (total gm, total wm and CFS). In the
> ROIs analysis, I use eTVI to control for for head size
> variability. Now my question is: should I control for head size
> when measuring overall brain atrophy? Theoretically speaking I'm
> not sure. Practically speaking there is a high positive
> correlation (as expected) between global brain measures and
> eTVI in my sample so I think it wouldn't be correct to use eTVI.
> But still, is global atrophy affected by head size? should I
> control for it?
>
> Second quick question: I'm planning to replicate the analysis
> measuring thickness differences. Should I control for tot mean
> thickness then?
>
> Thanks in advance for your help.
>
> Gloria
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> 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

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Re: [Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

Great - thanks.
It's running.
I see several warnings which I presume can be ignored:
hostname: Name or service not known

Best - Don


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia
Sent: Tuesday, April 10, 2018 4:24 PM
To: freesurfer 
Subject: Re: [Freesurfer] newbie trac-all -bedp question


Hi Don - See: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html



Best,

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
>
 on behalf of Krieger, Donald N. >
Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question


I am getting the following output with error on this command:



trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23


INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131: 
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected



I apologize for not finding the answer in the list archive.

It's probably there.



I'm running under ubuntu 14.04.



bedpostx_mgh is a shell script which calls for /bin/sh.

On my machine, that is a symlink to /bin/bash

If I change it to be explicitly /bin/bash, it runs a bit further.

Here is the full output:


INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
subjectdir is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
Making bedpostx directory structure
Queuing preprocessing stages
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
Queuing parallel processing stage
0 slices processed
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
Queuing post processing stage
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: line 439: 26461 Terminated  
${subjdir}.bedpostX/monitor



Thanks - Don


___
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.

Re: [Freesurfer] newbie trac-all -bedp question

[Yendiki, Anastasia]

Hi Don - See: 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html


Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Krieger, Donald N. 

Sent: Tuesday, April 10, 2018 1:15:05 PM
To: freesurfer
Subject: [Freesurfer] newbie trac-all -bedp question


I am getting the following output with error on this command:


trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23


INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131: 
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected


I apologize for not finding the answer in the list archive.

It's probably there.


I'm running under ubuntu 14.04.


bedpostx_mgh is a shell script which calls for /bin/sh.

On my machine, that is a symlink to /bin/bash

If I change it to be explicitly /bin/bash, it runs a bit further.

Here is the full output:


INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
subjectdir is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
Making bedpostx directory structure
Queuing preprocessing stages
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
Queuing parallel processing stage
0 slices processed
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
Queuing post processing stage
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: line 439: 26461 Terminated  
${subjdir}.bedpostX/monitor



Thanks - Don

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Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

[Hoopes, Andrew]

The fix that Anna needs was committed last Friday.
Andrew

From:  on behalf of "Dicamillo, Robert" 

Reply-To: FS Help 
Date: Tuesday, April 10, 2018 at 12:27 AM
To: FS Help 
Cc: "Dicamillo, Robert" 
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate memory)

If you are running on Ubuntu, I have a build of the freesurfer source checked
out from about one month ago (March 9th) that I did on an Ubuntu 16.04 system 
using gcc 4.9.

However,  I did not have the test data to run tests, so I must add the 
disclaimer that the binaries
have not gone thru the usual tests.  But if you want to try it, you can download
the compressed ~2G archive from the link below.  It is an archive of the 
./install
tree with ./bin, ./lib, etc.

https://drive.google.com/file/d/1hWs3gdfVExRMW5nl-aufQyMX8yWSHi8Y/view?usp=sharing

- rob

On Apr 9, 2018, at 2:31 PM, Hoopes, Andrew 
> wrote:

Hi Anna,

Unfortunately, we’re not able to build the dev code right now due to a compile 
error, but this should get sorted out within the next day or two, so I can help 
you out with getting this new mri_normalize then

best
Andrew

From: 
>
 on behalf of Anna Daniels 
>
Reply-To: FS Help 
>
Date: Monday, April 9, 2018 at 1:10 PM
To: FS Help 
>
Subject: Re: [Freesurfer] recon-all: exited with errors (white matter peak at 
110, cannot allocate memory)

Hi Bruce,
thank you for the quick reply!
Ubuntu 16.04 LTS 64-bit
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Please let me know how to incorporate the new version into the installation.
Thank you very much and best,
Anna


Hi Anna

no attachments :<

Srishti's issue stemmed from control points outside of the head. The
current (dev) version of mri_normalize detects and removes them. Can you
grab a new version of mri_normalize and see if it fixes your problem? Let
us know your hardware/software environment and we will get it to you

cheers
Bruce


On Fri, 6 Apr 2018, Anna Daniels wrote:

> Hi Bruce, hi Srishti,
>
> I have exactly the same problem with several subjects rerunning recon-all
> and there was sufficient memory available. I also tried out the last command
> directly which resulted in the same error log.
>
> ?mri_normalize 
> -f/home/anna/FREESURFER/00_DATA_MABT1T2/02a_MABT1T2_cross_edits_transfer/rrer
> uncrosstest_cp17/22275_T1_fs_edit/tmp/control.dat -mprage -aseg
> aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
>
> Attached you can find the input file.
>
> Thank you and best,
> Anna?[icon_10_generic_list.png] ?22275_T1_fs_edit.zip[IMAGE]
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Re: [Freesurfer] how to control for head size differences when measuring global atrophy?

[Maria Gloria Rossetti]

Thanks for getting back to me. 
My hp is the same as for the volumetric analysis. I want to measure thickness 
differences between patients and controls while controlling for major 
confounders (head size included). However , since thickness doesn't scale with 
eTIV as much as volume how can I control for head size variability? What would 
you suggest me to do? I am not that familiar with thickness analysis and I 
would not add unnecessary noise. 

Best, 
Gloria 

(n.b. in my sample, eTIV is significantly different between groups) Best, 



Da: "Douglas Greve"  
A: "freesurfer"  
Inviato: Martedì, 10 aprile 2018 16:24:42 
Oggetto: Re: [Freesurfer] how to control for head size differences when 
measuring global atrophy? 



I would probably correct total GM, total WM, and total ventricular CSF by head 
size. It is not surprising that they covary a lot (as you point out). But what 
you want is what is left over after you remove the effect. You can also divide 
by the eTIV rather than regressing it out, but the results will be similar. 

As for thickness, many people regress out the mean thickness, but this changes 
the hypothesis that you are testing (and so the interpretation of the results). 
As such, this is a question that you will have to answer yourself. 

On 4/9/18 10:11 AM, Maria Gloria Rossetti wrote: 



Dear freesurfers 

my study aims to measure volumetric differences between patients X and 
controls. As dependent variables, I have (i) a-priori ROIs and (ii) global 
brain measures (total gm, total wm and CFS). In the ROIs analysis, I use eTVI 
to control for for head size variability. Now my question is: should I control 
for head size when measuring overall brain atrophy? Theoretically speaking I'm 
not sure . Practically speaking there is a high positive correlation (as 
expected) between global brain measures and eTVI in my sample so I think it 
wouldn't be correct to use eTVI. But still, is global atrophy affected by head 
size? should I control for it? 

Second quick question: I'm planning to replicate the analysis measuring 
thickness differences. Should I control for tot mean thickness then? 

Thanks in advance for your help. 

Gloria 


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[Freesurfer] MCR

[John Absher]

Hi,

I was pleased to learn freesurfer runs with the standalone matlab runtime, and 
installed this on CentOS7. It seems to be working well. I noticed that there's 
also a version of spm12 that runs using this runtime, "with limitations." Two 
questions:


1.  Are there freesurfer limitations using this runtime that can be 
overcome by having the full matlab version installed?

2.  Can I use the same runtime I've already installed for freesurfer to run 
spm12, or will I need a new one?

Thanks,

John

John R. Absher, MD, FAAN
GHS Neurosciences
jabs...@ghs.org
864-350-6655 (mobile)

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Re: [Freesurfer] recon-all | ln -s error

[Antonin Skoch]

Dear Pradeep,
this issue has appeared several times already here. See following thread:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52560.html
Antonin Skoch

Hello All, My $SUBJECTS_DIR is located on an external disk that was mounted and 
recon-all exited with errors at ln -s lh.white.preaparc.H lh.white.HI was not 
able to perform this operation with sudo as well 4172_vsl/surf$ sudo ln -s 
lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': 
Operation not supported but cp works 4172_vsl/surf$ cp lh.white.preaparc.H 
lh.white.H has any one come across this problem and what is the best way to fix 
this? Thanks, Pradeep


Hello All,

My $SUBJECTS_DIR is located on an external disk that was mounted and
recon-all exited with errors at ln -s lh.white.preaparc.H lh.white.HI was not 
able to perform this operation with sudo as well

4172_vsl/surf$ sudo ln -s lh.white.preaparc.H lh.white.H
ln: failed to create symbolic link 'lh.white.H': Operation not supported

but cp works
4172_vsl/surf$ cp lh.white.preaparc.H lh.white.H

has any one come across this problem and what is the best way to fix this?

Thanks,
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[Freesurfer] newbie trac-all -bedp question

[Krieger, Donald N.]

I am getting the following output with error on this command:


trac-all -bedp -s HDFT1001 -i ep2d_diff_SliceAcc_b1k_64_768x768.23


INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: 131: 
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected


I apologize for not finding the answer in the list archive.

It's probably there.


I'm running under ubuntu 14.04.


bedpostx_mgh is a shell script which calls for /bin/sh.

On my machine, that is a symlink to /bin/bash

If I change it to be explicitly /bin/bash, it runs a bit further.

Here is the full output:


INFO: SUBJECTS_DIR is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
INFO: Diffusion root is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects
Actual FREESURFER_HOME /media/portable/home/kriegerd/Contrib/Freesurfer_6.0
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
subjectdir is 
/media/portable/home/kriegerd/Contrib/Freesurfer_6.0/subjects/HDFT1001/dmri
Making bedpostx directory structure
Queuing preprocessing stages
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
Queuing parallel processing stage
0 slices processed
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
Queuing post processing stage
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: 470: 
/home/kriegerd/Contrib/Freesurfer/bin/fsl_sub_mgh: Syntax error: "(" unexpected 
(expecting ";;")
/home/kriegerd/Contrib/Freesurfer/bin/bedpostx_mgh: line 439: 26461 Terminated  
${subjdir}.bedpostX/monitor



Thanks - Don

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[Freesurfer] Creating average surface for fMRI subjects and extracting cortical thickness

[Arsenije Subotic]

Dear experts,


I would like to create an average surface template of fMRI activation for two 
groups, and then determine areas of low cerebrovascular reactivity in my 
disease group, create a ROI, and extract the cortical thickness in this region 
and see how it compares to a control group by translating this ROI onto the 
control surface template. Do you have any tips or suggestions on how this 
workflow should be done?


I've currently been able to create an average surface for both groups, and I 
know how to create labels using tksurfer and to extract cortical thickness 
using mri_anatomical_stats. Is it possible however to create an ROI by only 
considering areas of low CVR/low activation in my disease group and calculating 
cortical thickness for this area, and then visualize it somehow and then 
translate this label onto the control group and doing the same?


I know it's a lot of questions, but going through the tutorial 
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_tktools)
 it seems that I wasn't able to find exactly what I'm looking for.


Thank you for your help,

Arsenije

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Re: [Freesurfer] how to control for head size differences when measuring global atrophy?

[Douglas Greve]

I would probably correct total GM, total WM, and total ventricular CSF 
by head size. It is not surprising that they covary a lot (as you point 
out). But what you want is what is left over after you remove the 
effect. You can also divide by the eTIV rather than regressing it out, 
but the results will be similar.


As for thickness, many people regress out the mean thickness, but this 
changes the hypothesis that you are testing (and so the interpretation 
of the results). As such, this is a question that you will have to 
answer yourself.



On 4/9/18 10:11 AM, Maria Gloria Rossetti wrote:

Dear freesurfers

my study aims to measure volumetric differences between patients X and 
controls. As dependent variables, I have (i) a-priori ROIs and (ii) 
global brain measures (total gm, total wm and CFS). In the ROIs 
analysis, I use eTVI to control for for head size variability. Now my 
question is: should I control for head size when measuring overall 
brain atrophy? Theoretically speaking I'm not sure. Practically 
speaking there is a high positive correlation (as expected) between 
global brain measures and eTVI in my sample so I think it wouldn't be 
correct to use eTVI. But still, is global atrophy affected by head 
size? should I control for it?


Second quick question: I'm planning to replicate the analysis 
measuring thickness differences. Should I control for tot mean 
thickness then?


Thanks in advance for your help.

Gloria


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Re: [Freesurfer] -make all flag

[Douglas Greve]

It only looks at file time stamps. It knows the order in which files 
should be created. If it sees the time staamps are out of order, then it 
re-runs the processes needed to put them in order. You will have to 
include any special flags like -mprage



On 4/10/18 9:42 AM, Boerwinkle, Anna wrote:


Hi,


I was wondering if you could explain the -make all flag. When you use 
it with recon-all to rerun after edits, does it determine where to 
start the recon-all process based on the stamps of the edited files? 
And if I use other flags (such as -mprage) when I initially ran 
recon-all, do I need still include those when I rerun with -make all 
or can -make all also determine and automatically apply the flags I used?



Thank you very much for your help!


Anna

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Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

[Douglas Greve]

They are not in registration. Try running bbregister to create a 
registration file (lta), then pass the lta to tkregisterfv instead of 
--regheader



On 4/9/18 11:49 PM, Bruce Fischl wrote:
How did you generate the registration? And give us the details of what 
you are trying to register

Cheers
Bruce

On Apr 8, 2018, at 2:55 PM, srishti goel <23srishtig...@gmail.com 
> wrote:



Hi Bruce,

Thanks so much for pointing that out, I totally missed that part.

Also, the registration definitely isn't appropriate.
Could someone please guide me how to correct this problem. I have 
attached a screenshot of how it looks like currently.





Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12


On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl 
> wrote:


Hi Srishti

the directory you are in doesn't matter. YOu either need to set
SUBJECTS_DIR in the environment, or use --sd  to
specify the
directory that contains your subjects. I think you can also give
it the full path to a target volume if you want, but maybe Doug
can comment as he knows this stuff better than I do

cheers
Bruce



 On Sun, 8 Apr 2018, srishti goel wrote:

When I type this command:tkregisterfv --mov
negative_allsocial_proportion.nii --regheader --s
mni152_subject --surfs --reg reg.deleteme.dat

It gives me the error: cannot find mni152_subject.
Although I clearly checked that the directory from which I
am submitting this command has the
mni152_subject directory within which there are all the other
required directories such as: mri,
stats, surf, scripts, etc.

I am unsure what is happening here.


Best,
Srishti
Social/Clinical Research Specialist
Child Imaging Research and Life Experiences Lab
University of North Carolina at Chapel Hill
email (W): srish...@email.unc.edu 
skype: srishti.goel12


On Thu, Apr 5, 2018 at 12:49 PM, Douglas N. Greve
> wrote:
      Those commands look ok. My suspicion goes to the use of
--regheader. See
      whether the registration is ok with

      tkregisterfv --mov negative_allsocial_proportion.nii
--regheader --s
      mni152_subject --surfs --reg reg.deleteme.dat


      On 04/05/2018 08:34 AM, srishti goel wrote:
      > Hi,
      >
      > I am trying to compare my volume maps
      > (negative_allsocial_proportion.nii) to someone else's
      > (SN_like_cortical_lh.nii.gz) who have it on a surface
      > (mni152_subject). So I used the steps for
mri_vol2surf command as
      > follows:
      >
      > Commands:
      > mri_vol2surf --src negative_allsocial_proportion.nii
--regheader
      > mni152_subject --hemi lh --o ./neg_allsocial_lh.nii
--projfrac 0.5
      > Then to view it:
      > tksurfer mni152_subject lh inflated -overlay
./neg_allsocial_lh.nii
      > -overlay SN_like_cortical_lh.nii.gz -fthresh 0.5
      >
      > Everything ran fine and we didn't get any error but
then while viewing
      > the files we could not see our map
(neg_allsocail_lh.nii) on the
      > surface. This file seemed to work fine as it is not
an empty file when
      > I checked the file size. However, when we view it
using tksurfer it
      > does not show up as a highlighted portion on the
surface. The
      > SN_like_cortical_lh.nii.gz file shows up just fine.
      >
      > Could someone please help me figure out what might
have gone wrong here.
      >
      > Thanks so much!
      >
      >
      >
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Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

[Kaushal, Mayank]

I appreciate your providing the pros and cons associated with both options.

Lets say for now we want to pursue option 2. 

My understating is that since you recommend not to include ‘visit’ and 
'time_from_baseline’ in the same model, one of the steps in creating MLE model 
for option 2 would be to not include ‘time_from_baseline’ as a random variable.

As for any other considerations to be kept in mind while creating the LME model 
for option 2, kindly provide your thoughts on the matter.

Mayank
> On Apr 10, 2018, at 8:56 AM, Diers, Kersten /DZNE  
> wrote:
> 
> ATTENTION: This email originated from a sender outside of MCW. Use caution 
> when clicking on links or opening attachments.
> 
> 
> On Mo, 2018-04-09 at 19:53 +0200, Kaushal, Mayank wrote:
>> I am indeed considering LME model since I have multiple visits (4)
>> for each subject and multiple groups (3).
>> 
>> Based on your response, I am inclined to include the following.
>> 
>> Intercept - random variable
>> Slope (time_base_scan) - random variable
>> 
>> As I am including time_base_scan as the random variable, this should
>> take care of the timing information. Am I correct in making this
>> assumption?
>> 
>> Moving on to the categorical variables - group and visit.
>> I want to evaluate the following effects
>> 1. group
>> 2. visit
>> 3. group and visit
>> 
>> My concern here is how do I design the contrast matrix for this?
> 
> Let's consider the model first:
> 
> I would not recommend to include both 'visit' and 'time_from_baseline'
> in the same model. This is because these two variables should be highly
> correlated, and such a redundancy may make the estimation and
> interpretation of the model difficult. Therefore it is better to
> include just one of them, but not both.
> 
> So the basic decision would be whether to treat time 1) as continuous
> (then use 'time_from_baseline') or 2) as categorical (then use
> 'visit'):
> 
> In my eyes, there are advantages and disadvantages to both, see below.
> Regardless of that, in both cases it will be possible to assess the
> effects of group, time/visit, and their combination (e.g. different
> slopes between groups, or presence of group differences only at some
> visits but not all).
> 
> Option 1)
> 
> Using 'time_from_baseline', and hence treating time as continuous,
> gives the LME model that we have been discussing so far. So there is no
> need to create a new model, and as far as I can see, your research
> questions can already be answered with the current model.
> 
> Although it will not be possible to directly contrast, say, visit 1 and
> 2 with this approach, you will still be able to make statements like
> 'Per 1 year (or 2 years, or 1 month, or whatever unit of time,
> depending on your observation period), we expect changes of magnitude X
> (or 2*X, or X/12, ...) , according to this model', and this may even be
> more accurate than expressing change in units of visits. Note, though,
> that these changes will be modeled as linear changes across time
> (unless you include additional e.g. quadratic terms in the model).
> 
> Option 2)
> 
> Using 'visit', and hence treating time as categorical, would result in
> a model like a repeated-measures ANOVA. The main advantages, in my
> eyes, would be that you could explicitly compare between, say, visit 1
> and 2, or 1 and 4, etc. So, the categorical model may be a little bit
> easier to interpret, which is possibly another advantage.
> 
> A disadvantage of this option is that you'd need to specify a new
> model. As far as I can see, the LME framework can also cover the
> categorical scenario, but I'd need to check how. Otherwise, one could
> use a classical repeated-measures ANOVA 
> (https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard=DwIGaQ=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y=RqvEwdmcEg_aWsE7PBL80w=-Af3jZoZfdj4DqYkb4qhihYoKqoeJSRABuMScq6Q2QU=2PGnRH6-RPzAAOmDaTj8n8GWK1AH-vVxIKYjvQubYTg=
> .edu/fswiki/RepeatedMeasuresAnova). Another disadvantage is that the
> categorical approach discards information about the precise timing, and
> that it makes the assumption that the visits occurred at comparable
> time intervals across subjects.
> 
> I thought it would be good to lay out the two main modeling options, as
> they appear to me now, before proceeding.
> 
> Best,
> 
> Kersten
> 
> 
> 
> 
>> I am aware that I have asked more than my fair share of questions and
>> very grateful to you for being exceedingly patient in answering them.
>> 
>> Mayank
>>> 
>>> On Apr 9, 2018, at 12:15 PM, Diers, Kersten /DZNE >> ne.de> wrote:
>>> 
>>> ATTENTION: This email originated from a sender outside of MCW. Use
>>> caution when clicking on links or opening attachments.
>>> 
>>> 
>>> Hello,
>>> 
>>> this is somewhat difficult to answer, so the following is a
>>> personal
>>> opinion.
>>> 
>>> I think the first question is 

Re: [Freesurfer] Running Linear Mixed Effects (LME) Model

[Diers, Kersten /DZNE]

On Mo, 2018-04-09 at 19:53 +0200, Kaushal, Mayank wrote:
> I am indeed considering LME model since I have multiple visits (4)
> for each subject and multiple groups (3).
>
> Based on your response, I am inclined to include the following.
>
> Intercept - random variable
> Slope (time_base_scan) - random variable
>
> As I am including time_base_scan as the random variable, this should
> take care of the timing information. Am I correct in making this
> assumption?
>
> Moving on to the categorical variables - group and visit.
> I want to evaluate the following effects
> 1. group
> 2. visit
> 3. group and visit
>
> My concern here is how do I design the contrast matrix for this?

Let's consider the model first:

I would not recommend to include both 'visit' and 'time_from_baseline'
in the same model. This is because these two variables should be highly
correlated, and such a redundancy may make the estimation and
interpretation of the model difficult. Therefore it is better to
include just one of them, but not both.

So the basic decision would be whether to treat time 1) as continuous
(then use 'time_from_baseline') or 2) as categorical (then use
'visit'):

In my eyes, there are advantages and disadvantages to both, see below.
Regardless of that, in both cases it will be possible to assess the
effects of group, time/visit, and their combination (e.g. different
slopes between groups, or presence of group differences only at some
visits but not all).

Option 1)

Using 'time_from_baseline', and hence treating time as continuous,
gives the LME model that we have been discussing so far. So there is no
need to create a new model, and as far as I can see, your research
questions can already be answered with the current model.

Although it will not be possible to directly contrast, say, visit 1 and
2 with this approach, you will still be able to make statements like
'Per 1 year (or 2 years, or 1 month, or whatever unit of time,
depending on your observation period), we expect changes of magnitude X
(or 2*X, or X/12, ...) , according to this model', and this may even be
more accurate than expressing change in units of visits. Note, though,
that these changes will be modeled as linear changes across time
(unless you include additional e.g. quadratic terms in the model).

Option 2)

Using 'visit', and hence treating time as categorical, would result in
a model like a repeated-measures ANOVA. The main advantages, in my
eyes, would be that you could explicitly compare between, say, visit 1
and 2, or 1 and 4, etc. So, the categorical model may be a little bit
easier to interpret, which is possibly another advantage.

A disadvantage of this option is that you'd need to specify a new
model. As far as I can see, the LME framework can also cover the
categorical scenario, but I'd need to check how. Otherwise, one could
use a classical repeated-measures ANOVA (https://surfer.nmr.mgh.harvard
.edu/fswiki/RepeatedMeasuresAnova). Another disadvantage is that the
categorical approach discards information about the precise timing, and
that it makes the assumption that the visits occurred at comparable
time intervals across subjects.

I thought it would be good to lay out the two main modeling options, as
they appear to me now, before proceeding.

Best,

Kersten




> I am aware that I have asked more than my fair share of questions and
> very grateful to you for being exceedingly patient in answering them.
>
> Mayank
> >
> > On Apr 9, 2018, at 12:15 PM, Diers, Kersten /DZNE  > ne.de> wrote:
> >
> > ATTENTION: This email originated from a sender outside of MCW. Use
> > caution when clicking on links or opening attachments.
> > 
> >
> > Hello,
> >
> > this is somewhat difficult to answer, so the following is a
> > personal
> > opinion.
> >
> > I think the first question is whether your would like to go for a)
> > a
> > cross-sectional design or b) a longitudinal design.
> >
> > If a), you'd have a single scan per subject (e.g., baseline) and
> > could
> > discard the temporal information. So if you do not have a
> > longitudinal
> > research question and your goal is to model group differences at a
> > single time-point, it is not necessary (and overly complicated,
> > actually) to use a LME model.
> >
> > If b), you'd have multiple scans per subject, and would therefore
> > use
> > the LME model. I would not recommend to exclude the timing
> > information
> > from the model / design matrix in this case, no matter how close
> > the
> > temporal spacing may be. It is still possible to test for effects
> > other
> > than time, e.g. for group differences at baseline.
> >
> > Best regards,
> >
> > Kersten
> >
> > On Mi, 2018-04-04 at 23:37 +0200, Kaushal, Mayank wrote:
> > >
> > > The continuous variable in my analysis is time_base_scan with the
> > > time points evaluated by me being of acute and subacute nature.
> > > However, due to the small differences in time elapsed between
> > > 

[Freesurfer] -make all flag

[Boerwinkle, Anna]

Hi,


I was wondering if you could explain the -make all flag. When you use it with 
recon-all to rerun after edits, does it determine where to start the recon-all 
process based on the stamps of the edited files? And if I use other flags (such 
as -mprage) when I initially ran recon-all, do I need still include those when 
I rerun with -make all or can -make all also determine and automatically apply 
the flags I used?


Thank you very much for your help!


Anna


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Re: [Freesurfer] FSGD design for multi-centre study

[C.P.E. Rollins]

Thanks for your help. I've noticed, however, that 2 of the centres 
contribute a smaller number of subjects and don't in fact have any 
female controls. Should I remove these as classes (ie. take out 
control_Female_centre1 and control_Female_centre2) and then change the 
subsequent contrast file to look like:
1 1 1 1 1 1 1 1 1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0
Or would this be a problem since now the number of classes that are 
controls or patients are uneven (10 vs. 12)?

Thanks again,
Colleen

---
Colleen Rollins, PhD Candidate
Department of Psychiatry
University of Cambridge
Herchel Smith Building, Robinson Way, Cambridge CB2 0SZ

On 2018-04-09 14:50, C.P.E. Rollins wrote:
> Hi Douglas,
> 
> Thanks for your response. I just wanted to confirm how the FSGD and
> contrast files might look for the multicentre study. If I'm to create
> a separate class for each combination of diagnosis, sex, and center,
> would there then be 24 classes? (as there are 2 diagnoses (patient vs.
> control), 2 sex, and 6 centres).
> For instance:
> GroupDescriptorFile 1
> Group control_Male_centre1
> Group control_Female_centre1
> Group control_Male_centre2
> Group control_Female_centre2
> Group control_Male_centre3
> Group control_Female_centre3
> Group control_Male_centre4
> Group control_Female_centre4
> Group control_Male_centre5
> Group control_Female_centre5
> Group control_Male_centre6
> Group control_Female_centre6
> Group patient_Male_centre1
> Group patient_Female_centre1
> Group patient_Male_centre2
> Group patient_Female_centre2
> ...
> 
> Then, my contrast between patients and controls would look like
> 1 1 1 1 1 1 1 1 1 1 1 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0
> for a doss model, if I'm additionally controlling for age, or 24 zeros
> (instead of 1) for a dods model?
> Moreover, should I expect any issues with using such a high number of 
> classes?
> 
> Thanks again,
> Colleen
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