[Freesurfer] FreeSurfer downloading

[Sahil Bajaj]

Hi there,

This is SAHIL BAJAJ, a postdoc fellow from Houston Methodist Research
Institute. I have been trying to download Freesurfer for my linux machine
but somehow the link on the website- http://freesurfer.net/fswiki/Download
is not opening, I would really appreciate any help.

Thanks,
Sahil

-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.ne...@gmail.com 
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[Freesurfer] Segmentation fault: Core dumped

[Sahil Bajaj]

Hello FS experts,

I am running a command "fcseed-sess -s S01 -cfg abc.config" to get *.dat
file for further analysis. I used the same steps to calculate FC for 40
subjects, all steps run fine with 38 subjects but for 2 subjects I am
getting an error: Segmentation fault: Core dumped.

I checked the segmentation of anatomical data (generated using recon-all),
and it looks fine to me.
Here I am also attaching the log file created when I run this command.

Any help would be really appreciated.

Thanks,
Sahil
-- 
-----
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 


dat.log
Description: Binary data
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[Freesurfer] Cortical thickness using freesurfer

[Sahil Bajaj]

Dear all,

I am working on calculation of cortical thickness from a set of subjects. I
am following the instructions from
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness and I
am able to run up-to step-2 successfully i.e. I can display the ROIs on
fsaverage subject volume. But when I run step-3 using:

*mri_vol2surf --mov /media/Storage/FTD_Data/S01_LP/mri/lh_cuneus.nii --reg
TT.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out ROI5.mgh
--reshape*


It runs as follow:

(here lh_cuneus.nii is one of the ROIs,FTD_Data is my subject directory for
FreeSurfer and S01_LP is the output folder for one of the subjects after
running recon -all)


srcvol = /media/Storage/FTD_Data/S01_LP/mri/lh_cuneus.nii
srcreg = TT.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
ProjDist = 0.5
reshape = 1
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Reading surface /media/Storage/FTD_Data/fsaverage/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 1
using old
 2 0.1 0 1
using old
 3 0.2 0 1
using old
 4 0.3 0 1
using old
 5 0.4 0 1
using old
 6 0.5 0 1
using old
 7 0.6 0 1
using old
 8 0.7 0 1
using old
 9 0.8 0 1
using old
10 0.9 0 1
using old
Done mapping volume to surface
Number of source voxels hit = 75054
Reshaping 7 (nvertices = 163842)
Writing to ROI5.mgh
Dim: 23406 1 7


Although I don't see any error here but when I display using:

*tksurfer fsaverage lh inflated -overlay ROI5.mgh -fthresh 0.5*

it runs as follow:

setting fthresh to 0.5000
subject is fsaverage
hemiis lh
surface is inflated
surfer: current subjects dir: /media/Storage/FTD_Data
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /media/Storage/FTD_Data/fsaverage/surf
checking for nofix files in 'inflated'
Reading image info (/media/Storage/FTD_Data/fsaverage)
Reading /media/Storage/FTD_Data/fsaverage/mri/orig.mgz
surfer: Reading header info from
/media/Storage/FTD_Data/fsaverage/mri/orig.mgz
surfer: vertices=163842, faces=327680
tkmedit: Trying to open ROI5.dat
surfer: Interpreting overlay volume ROI5.mgh as encoded scalar volume.
surfer: curvature read: min=-0.673989 max=0.540227
surfer: single buffered window
surfer: tkoInitWindow(fsaverage)
surfer: using interface
/home/sahil/Softwares/freesurfer/tktools/tksurfer.tcl
Reading /home/sahil/Softwares/freesurfer/tktools/tkm_common.tcl
Reading /home/sahil/Softwares/freesurfer/tktools/tkm_wrappers.tcl
Reading /home/sahil/Softwares/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /home/sahil/Softwares/freesurfer/tktools/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...


Again, I don't see any error here. But ROI ROI5.mgh is not displayed on the
fsaverage surface. I tried to overlay ROI5.mgh on lh inflated using
freeview as well but ROI5.mgh is nowhere.


I would really appreciate any help.


Thanks,
Sahil
-- 
-----
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
Office: 713-363-9003
E-mail:sahil.ne...@gmail.com 
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[Freesurfer] Cortical thickness last step

[Sahil Bajaj]

Hello again,


To calculate cortical thickness, I am running step-4 & 5 following the
instructions from
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness


So running step 4:

*mri_surf2surf --s S01_LP --trgsubject fsaverage --hemi lh --sval
lh.thickness --tval lh.thickness.fsaverage.mgh --reshape*

where S01_LP is my subject ID, it runs as follow:


srcsubject = S01_LP
srcval = lh.thickness
srctype=
trgsubject = fsaverage
trgval = lh.thickness.fsaverage.mgh
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
Reading source surface reg /media/Storage/FTD_Data/S01_LP/surf/lh.sphere.reg
Loading source data
Reading target surface reg
/media/Storage/FTD_Data/fsaverage/surf/lh.sphere.reg
Done
Mapping Source Volume onto Source Subject Surface
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (98973)
Reverse Loop had 7939 hits
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
nTrg121 = 157350, nTrgMulti =  6492, MnTrgMultiHits = 2.22289
nSrc121 = 49582, nSrcLost = 0, nSrcMulti = 49391, MnSrcMultiHits =
2.47411
Saving target data
Reshaping 6 (nvertices = 163842)
Saving to lh.thickness.fsaverage.mgh


Next when I run step 5 as follow:

*mri_segstats --seg /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh --in
lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt*

It runs as follows:

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --seg /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh
--in lh.thickness.fsaverage.mgh --sum segstats-ROI5.txt
sysname  Linux
hostname degas
machine  x86_64
user sahil
UseRobust  0
Loading /media/Storage/FTD_Data/fsaverage/surf/ROI5.mgh
Loading lh.thickness.fsaverage.mgh
ERROR: dimension mismatch between input volume and seg
  input 27307 1 6
  seg   23406 1 7

As mentioned in the instructions I also tried using --reshape-factor 7 in
step 4 also but still I get exactly same error after running step 5. Could
you please help me in figuring out this problem?

Thanks,
Sahil
-- 
-----
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
Office: 713-363-9003
E-mail:sahil.ne...@gmail.com 
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[Freesurfer] Using qdec to view cluster results

[Sahil Bajaj]

Dear all,

I have a very basic question regarding the usage of qdec.
I am using qdec to view cortical thickness for a set of patients vs.
controls. I am able to create table.dat, design the comparison and display
the results. After that, my results are saved as sig.mgh in qdec folder.
Now when I try to reopen the same results by loading surface and overlaying
with sig.mgh, although it shows me the results but when I click on 'Find
Clusters and go to max' it gives me following error:
Error generating cluster stats GeneratingClusterStats: white surface was
not found

and it doesn't display any cluster results in terminal window. If I do
everything from very first step, starting from loading table.dat, creating
design once again, everything is working fine.

I would really appreciate any help.

Thanks,
Sahil

-- 
---------
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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[Freesurfer] Cortical thickness average

[Sahil Bajaj]

Hello FreeSurfer community,

I calculated cortical thickness for 100 controls following the instructions
described here:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness

So I have 100 lh.thickness.fsaverage.mgh, one for each subject. I was
wondering if there is any way to average the thickness over these 100
lh.thickness.fsaverage.mgh files to get one final lh.thickness.fsaverage.mgh

I am interested in calculating cortical thickness for 15 previously defined
ROIs, but I do not want to calculate 15x100 text files using mri_segstats
i.e. 15 text files for each subject and then average over those but I would
rather prefer to average over 100 lh.thickness.fsaverage.mgh files first
and then calculate thickness for each ROI to get 11 text files.

Any help would be really appreciated.

Thanks,
Sahil
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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Re: [Freesurfer] Cortical thickness average

[Sahil Bajaj]

Thanks a lot Elijah, I will give a try to this and will surely get back to
you if I had any issue.

Thanks again for the help.

Regards,
Sahil

On Thu, Mar 24, 2016 at 6:39 PM, Elijah Mak  wrote:

> Hi Sahil,
>
> I did something similar recently. I believe you can use mri_concat with
> the -mean option to create an average map of the group.
>
> Another option might be make_average_subject?
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject
>
> Best Wishes,
> Elijah
>
>
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-- 
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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[Freesurfer] Qdec interface issue

[Sahil Bajaj]

Hello,

I am working on measuring cortical thickness of a patient group. I am using
Ubuntu 14.04

Somehow, if I use command line to perform the analysis, Freesurfer/qdec is
working fine but if I use Qdec interface, it works fine initially but when
I switch to display window, it doesn't allow me to change/edit FDR
p-values, threshold min and max, although I can click on all the options on
display window e.g. inflated, pial, white, etc.

Also, when I tried to do the same on other computer (Mac), it works fine
for me.

I was wondering if this is because of video card problem or something. The
thing is it was working before for some time, then after a computer crash,
it no longer works. We replaced the video card but are still experiencing
the same problem.

At this point I would welcome any suggestions.

Thanks,
Sahil

-- 
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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[Freesurfer] ROIs2Label

[Sahil Bajaj]

Dear FreeSurfer experts,

I have a surface ROI defined in MNI co-ordinate system, ROI.mgh, I am
interested in converting it into label. I tried following steps:
(1). mri_cor2label --i ROI.mgz --id 1 --l X.label
(2). mri_label2label --srclabel X.label --s fsaverage --trglabel Xnew.label
--hemi lh --paint 30

This gives me final .label file as Xnew.label, then I tried to check if
this is correct using:
(3). tksurfer fsaverage lh inflated -overlay ROI.mgh -fthresh 0.5
and then on top of it File>load label>Xnew.label

Now the new Xnew.label is not matching with ROI.mgz.
Can someone please help me to figure out what I am doing wrong here?
Also, how can I view the label in FreeView i.e. is there any way to load
this new label just like LookUp Table?

Thanks,
Sahil

-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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[Freesurfer] Normalization for functional connectivity

[Sahil Bajaj]

Hello all,

I am interested in importing some seed regions which are in MNI space in
order to calculate functional connectivity maps. Looks like command
preproc-sess doesn't normalize the BOLD data and only the regions generated
by FreeSurfer LookUp table which have 'segid', can be used to calculate
functional connectivity maps.

I was wondering how can I normalize the BOLD and T1w data so that I can use
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
instructions to calculate functional connectivity from MNI seed regions.

Thanks,
Sahil

-- 
---------
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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Re: [Freesurfer] Normalization for functional connectivity

[Sahil Bajaj]

Hi Dr. Greve,

This works for me if I define seeds into subject-wise anatomical space.

Now, location of seed regions across subjects might differ because these
are defined in subject-wise anatomical space. Hence subject-wise
connectivity maps are generated from subject-wise seeds but these can be
displayed only on fsaverage space, not on subject-wise space. That means
connectivity maps are normalized here and we can do 2nd level analysis
(keeping subject-wise seeds as subject-wise (not normalized)).

(a). If above points are correct, then it's fine to calculate 2nd level
maps but I am not sure how seeds can be overlaid on 2nd level maps or 1st
level maps because seeds are not normalized but both 1st and 2nd level
connectivity maps are. Is there any way I can make sure that self
connectivity is giving correlation coefficient ~1.
(b). If above points are incorrect i.e. if subject-wise connectivity maps
are not normalized and are in subject-wise space then (i) why can't we
overlay those on subject-wise connectivity maps on subject-wise surfaces
and (ii) how second level maps can be calculated from un-normalized
1st-level level maps?

For second level analysis, I am using isxconcat-sess and mri_glmfit.

Could you please clarify this for me?

Thanks,
Sahil

On Tue, May 10, 2016 at 10:44 AM, Douglas N Greve  wrote:

> You should map the ROI into the individual subject's anatomical space,
> the specify the ROI when you configure the seed (eg, fcseed-config -seg
> ROI.mgz -segid 1 ...)
>
> On 05/10/2016 10:37 AM, Sahil Bajaj wrote:
> > Hello all,
> >
> > I am interested in importing some seed regions which are in MNI space
> > in order to calculate functional connectivity maps. Looks like command
> > preproc-sess doesn't normalize the BOLD data and only the regions
> > generated by FreeSurfer LookUp table which have 'segid', can be used
> > to calculate functional connectivity maps.
> >
> > I was wondering how can I normalize the BOLD and T1w data so that I
> > can use
> >
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
> > instructions to calculate functional connectivity from MNI seed regions.
> >
> > Thanks,
> > Sahil
> >
> > --
> > -
> > Sahil Bajaj
> > Post-doctoral Fellow
> > Nantz National Alzheimer's Center, Department of Neurology
> > The Houston Methodist Research Institute (THMRI)
> > Houston, TX, USA.
> > E-mail:sahil.br...@gmail.com <mailto:e-mail%3asahil@gmail.com>
> >
> >
> > ___
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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
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> properly
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-- 
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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Re: [Freesurfer] Normalization for functional connectivity

[Sahil Bajaj]

I already used this argument during preprocessing.
According to the explanation here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
in step-3, time-series data are sampled onto fsaverage then I am not sure
why 2nd-level analysis is showing me significant self connectivity little
far from the seed regions which are in subject-wise anatomical space.

On Wed, May 11, 2016 at 3:08 PM, Martin Juneja  wrote:

> I would suggest you to check if preproc is done using the argument
> -mni-305-2mm.
>
> On Wed, May 11, 2016 at 12:48 PM, Sahil Bajaj 
> wrote:
>
>> Hi Dr. Greve,
>>
>> This works for me if I define seeds into subject-wise anatomical space.
>>
>> Now, location of seed regions across subjects might differ because these
>> are defined in subject-wise anatomical space. Hence subject-wise
>> connectivity maps are generated from subject-wise seeds but these can be
>> displayed only on fsaverage space, not on subject-wise space. That means
>> connectivity maps are normalized here and we can do 2nd level analysis
>> (keeping subject-wise seeds as subject-wise (not normalized)).
>>
>> (a). If above points are correct, then it's fine to calculate 2nd level
>> maps but I am not sure how seeds can be overlaid on 2nd level maps or 1st
>> level maps because seeds are not normalized but both 1st and 2nd level
>> connectivity maps are. Is there any way I can make sure that self
>> connectivity is giving correlation coefficient ~1.
>> (b). If above points are incorrect i.e. if subject-wise connectivity maps
>> are not normalized and are in subject-wise space then (i) why can't we
>> overlay those on subject-wise connectivity maps on subject-wise surfaces
>> and (ii) how second level maps can be calculated from un-normalized
>> 1st-level level maps?
>>
>> For second level analysis, I am using isxconcat-sess and mri_glmfit.
>>
>> Could you please clarify this for me?
>>
>> Thanks,
>> Sahil
>>
>> On Tue, May 10, 2016 at 10:44 AM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu> wrote:
>>
>>> You should map the ROI into the individual subject's anatomical space,
>>> the specify the ROI when you configure the seed (eg, fcseed-config -seg
>>> ROI.mgz -segid 1 ...)
>>>
>>> On 05/10/2016 10:37 AM, Sahil Bajaj wrote:
>>> > Hello all,
>>> >
>>> > I am interested in importing some seed regions which are in MNI space
>>> > in order to calculate functional connectivity maps. Looks like command
>>> > preproc-sess doesn't normalize the BOLD data and only the regions
>>> > generated by FreeSurfer LookUp table which have 'segid', can be used
>>> > to calculate functional connectivity maps.
>>> >
>>> > I was wondering how can I normalize the BOLD and T1w data so that I
>>> > can use
>>> >
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>>> > instructions to calculate functional connectivity from MNI seed
>>> regions.
>>> >
>>> > Thanks,
>>> > Sahil
>>> >
>>> > --
>>> > -
>>> > Sahil Bajaj
>>> > Post-doctoral Fellow
>>> > Nantz National Alzheimer's Center, Department of Neurology
>>> > The Houston Methodist Research Institute (THMRI)
>>> > Houston, TX, USA.
>>> > E-mail:sahil.br...@gmail.com <mailto:e-mail%3asahil@gmail.com>
>>> >
>>> >
>>> > ___
>>> > 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
>&g

[Freesurfer] Connectivity from external seeds

[Sahil Bajaj]

Hello FS experts,

I am sorry for reposting this question in the forum:

I calculated subject-wise resting-state FC maps after defining seeds into
subject-wise anatomical space as mentioned in the manual. Now, location of
seed regions across subjects differ a little.

According to manual, FS maps the time-series on fsaverage lh and rh
hemisphere. That means connectivity maps for each subject are registered to
fsaverage space and it should be fine to calculate 2nd level maps.

If that's correct then my questions are:
(a). How seeds can be overlaid on 2nd level maps or 1st level maps because
seeds are not in fsaverage space but both 1st and 2nd level connectivity
maps are. When I see subject-wise FC maps, those are little far from the
actual seed locations which I defined in subject-wise anatomical space.
(b). How FS deals with seed regions in terms of 2nd level analysis because
it calculates FC from seeds which are in subject-wise anatomical space but
it reports FC in fsaverage space, so 2nd level results are even more far
away from actual seed region locations?

I would really appreciate any thoughts/suggestions on this.

Thanks,
Sahil
-- 
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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[Freesurfer] Binary images multiplication

[Sahil Bajaj]

Hi,

I would like to multiply two binary images (standard brain image with an
ROI) using fslmaths (or may be using some other way) command. Although both
are in standard space but image dimensions are different. I was wondering
if there is any way I can do that without any co-registration step.

Thanks,
Sahil
-- 
-- 
-
Sahil Bajaj
Post-doctoral Fellow
Nantz National Alzheimer's Center, Department of Neurology
The Houston Methodist Research Institute (THMRI)
Houston, TX, USA.
E-mail:sahil.br...@gmail.com 
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[Freesurfer] ROIs in midline for cortical thickness

[Sahil Bajaj]

Hi everyone,

I have supplementary motor area (SMA) defined in standard MNI volume space
and I would like to extract cortical thickness for this area. I have 80% of
SMA in left hemisphere and 20% on right hemisphere. So I am stuck at the
command mri_vol2surf before proceeding to mri_segstats.

In mri_vol2surf, I am not sure what should I specify for --hemi i.e.
whether its left or right hemisphere (lh or rh). If I specify e.g. lh, then
would not it convert left hemisphere SMA voxels to surface and later on
extract the measure from left hemisphere only and vice-versa for right
hemisphere.

I am not sure how would that work if portion of ROI is on both hemispheres
and how can I run mri_vol2surf command?

Thanks,
Sahil
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Re: [Freesurfer] ROIs in midline for cortical thickness

[Sahil Bajaj]

Thanks Dr. Fischl. I will surely give a try to this.

On Wed, Feb 1, 2017 at 3:17 PM, Bruce Fischl 
wrote:

> I see. Have you run recon-all on each hemi? If so, use bbregister to
> register the surfaces to the fmri data, then use mri_vol2surf to map the
> activations on to the left and right surfaces and draw your ROIs that way.
>
> cheers
>
> Bruce
> On Wed, 1 Feb 2017, Sahil Bajaj wrote:
>
> Hi Dr. Fischl,
>> Thank you so much for your reply.
>>
>> I have this SMA activation from a fMRI task. I am interested in getting
>> cortical thickness of exactly the same area. Its showing activation in
>> both
>> hemispheres. I am also attaching here screen shot to make it more clear
>> how
>> it looks like. To do that, thats correct, I am trying to draw both left
>> and
>> right SMA thickness.
>>
>> Thanks.
>>
>> On Wed, Feb 1, 2017 at 2:46 PM, Bruce Fischl 
>> wrote:
>>   Hi Sahil
>>
>>   can you clarify what you mean. Do you have the left hemi SMA
>>   labeled in MNI space and it (incorrectly) extends into the right
>>   hemi? Or are you trying to draw both the left and the right SMA?
>>
>>   Bruce
>>   On Wed, 1 Feb 2017, Sahil Bajaj wrote:
>>
>> Hi everyone,
>> I have supplementary motor area (SMA) defined in
>> standard MNI volume space
>> and I would like to extract cortical thickness for
>> this area. I have 80% of
>> SMA in left hemisphere and 20% on right hemisphere.
>> So I am stuck at the
>> command mri_vol2surf before proceeding to
>> mri_segstats.
>>
>> In mri_vol2surf, I am not sure what should I specify
>> for --hemi i.e. whether
>> its left or right hemisphere (lh or rh). If I
>> specify e.g. lh, then would
>> not it convert left hemisphere SMA voxels to surface
>> and later on extract
>> the measure from left hemisphere only and vice-versa
>> for right hemisphere.
>>
>> I am not sure how would that work if portion of ROI
>> is on both hemispheres
>> and how can I run mri_vol2surf command?
>>
>> Thanks,
>> Sahil
>>
>>
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>> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] Error viewing corrected results

[Sahil Bajaj]

Hello Martin and Antonin,

I was following this conversation very closely to understand how to use
PALM in FreeSurfer.

Can any of you please confirm in case I am interested in checking
correlation between gyrification index (LGI) and behavioral measure using
two tailed, p < 0.05:
Step 1: I used --cache 1.3
Step 2: Because (1-10^-1.3)= 0.95, so I will have to use -C 0.95 in palm
command

Could you please confirm if thats correct and the output *_tstat.mgz is the
final two-tailed corrected significant correlation map between LGI and
behavioral data?

Thanks a lot for this wonderful discussion.
Sahil

PS: For one-tailed: it will be -C -0.95 in palm command, correct?



On Tue, Mar 7, 2017 at 3:48 PM, Antonin Skoch  wrote:

> Dear Martin,
>
> after -s option, there have to be 2 arguments, as I specified in my previous 
> mail:
>
> -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh
>
> And beware that -C has to have negative sign, if your hypothesis is 
> one-tailed negative.
>
> Antonin
>
>
>
> Hi Antonin,
>
> Thank you so much for this detailed explanation, that's really useful.
>
> Following your instructions, I ran:
>
> palm -i lh.MEQ_LGI.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh -d
> check.csv -t Contrast_MEQ.csv -n 5000 -m lh.MEQ_LGI.glmdir/mask.mgh -o
> myresults -Cstat extent -C 3.719016
>
> but I am getting following error:
>
> Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with the following
> options:
> -i lh.MEQ_LGI.10.mgh
> -s fsaverage/surf/lh.white.avg.area.mgh
> -d check.csv
> -t Contrast_MEQ.csv
> -n 5000
> -m lh.MEQ_LGI.glmdir/mask.mgh
> -o myresults
> -Cstat extent
> -C 3.719016
> Loading surface 1/1: fsaverage/surf/lh.white.avg.area.mgh
> Reading input 1/1: lh.MEQ_LGI.10.mgh
>
> Struct contents reference from a non-struct array object.
>
> Error in palm_takeargs (line 1632)
> if any(size(plm.srf{s}.data.vtx,
> 1) == ...
>
> Error in palm_core (line 33)
> [opts,plm] = palm_takeargs(varargin{:});
>
> Error in palm (line 81)
> palm_core(varargin{:});
>
> Could you please help me in resolving this error?
>
> Thanks much.
>
> On Tue, Mar 7, 2017 at 2:55 PM, Antonin Skoch  wrote:
>
> > Dear Martin,
> >
> > input -i input file is
> >
> > lh.MEQ_LGI.10.mgh file in your glmdir directory (for left hemisphere).
> >
> > As you could read in following messages in the referenced thread in FSL
> > discussion forum, cluster-forming threshold need to be specified in z, not
> > in t.
> >
> > Therefore, you would have to select cluster forming threshold and specify
> > it as a z score.
> >
> > I think that your z-score for your original mri_glmfit-sim commandline
> > argument
> >
> > --cache 4 neg
> >
> > will be  -qnorm(1-10^-4)=-3.719016. (I am not perfectly sure since I never
> > tried negative one-side hypothesis testing in PALM).
> >
> > You could also use other statistics, such as cluster mass, or TFCE. See
> > PALM user guide.
> >
> > Do not include -pmethodp none and -pmethodr none, since you would need the
> > partitioning due your non-orthogonal design matrix.
> >
> > ?h.white.avg.area.mgh file (which you will find under fsaverage directory)
> > goes as second argument after -s option.
> >
> > Therefore I suppose the commandline for cluster extent inference with
> > cluster forming threshold p=0.0001, negative one-sided hypothesis, left
> > hemisphere, will be hopefully something like
> >
> > palm
> > -i y.mgh
> > -s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh
> > -d Xg.csv
> > -t your_contrasts.csv
> > -n number_of_permutations
> > -m mask.mgh
> > -o output_basename
> > -Cstat extent
> > -C -3.719016
> > -saveglm
> > -savedof
> > -savemetrics
> >
> > The last 3 commandline options are only for diagnostical purposes.
> >
> > The output is surface overlay you can visualize in freeview.
> >
> > I use following code snippet for the reporting significant clusters in MNI
> > coordinates:
> >
> > # PALM output cluster extent p maps have 1 outside cluster - problem with
> > mri_surfcluster and also for display in freeView
> > #here we set values 1 to 0 in pmaps.
> > #done by binarizing and subtracting
> > if [[ $# -ne 2 ]]; then
> > echo "get cluster summary of PALM statistics. Expecting 2 arguments: 1-
> > input p-map, 2- hemisphere (lh/rh)"
> > exit
> > fi
> > mri_binarize --i $1 --min 1 --o p_bin.mgz
> > mris_calc --output ${1%%.mgz}_filtered.mgz $1 sub p_bin.mgz
> > mri_surfcluster --in ${1%%.mgz}_filtered.mgz --subject fsaverage --hemi $2
> > --surf white --annot aparc --thmin 0.1 --thmax 0.05 --mask mask.mgh
> > --sum ${1%%.mgz}_cluster.summary --nofixmni
> > rm p_bin.mgz
> >
> > They are not Bonferroni-corrected for 2 hemispheres (--2spaces).
> >
> > Regarding your design and contrast:
> >
> > Design has to be matrix of values. You can use qdec to produce Xg.dat file
> > with design matrix, then rename it to Xg.csv to be correctly readable by
> > PALM.
> >
> > Regards,
> >
> > Antonin
> >
> >
> >
> >
> >
> > Hi Antonin,
> >
> > As you 

Re: [Freesurfer] Error viewing corrected results

[Sahil Bajaj]

Dear Antonin,

Setting minimum to 1.3 for *_clustere_tstat_fwep doesn't show any
significant cluster and similarly thresholded map *dpv_tstat.mgz also
doesn't show anything at -log10(0.05) = 1.3. As you said, it seems like
even though there is big cluster but after FWER correction, the
significance goes away. Actually, even when I removed -logp, I still do not
see any significant cluster.

Next, I tried to use mri_surfcluster using following three commands
following instructions from the link you sent:

mri_binarize --i Results_Left_clustere_tstat_fwep.mgz --min 1 --o p_bin.mgz

mris_calc --output pmap_filter.mgz Results_Left_clustere_tstat_fwep.mgz sub
p_bin.mgz

mri_surfcluster --in pmap_filter.mgz --subject fsaverage --hemi lh --surf
white --annot aparc.a2009s --thmin 0.0001 --thmax 0.05 --mask
glmdir/mask.mgh --sum summary --nofixmni

This gives me 'zero' cluster in the summary file.

If the above steps are correct, would you conclude that the LGI results are
not significant and un-reportable for publication purpose and I should give
a try to thickness, volume and area maps?

Thanks you so much Antonin for all your help.
Sahil



On Wed, Mar 8, 2017 at 3:05 PM, Antonin Skoch  wrote:

> Dear Sahil,
>
> If you used -logp as Anderson suggested, you should set your min to 1.3 to
> threshold your *_clustere_tstat_fwep map and see the clusters.
>
> What is the value of *_clustere_tstat_fwep in the region of the big
> cluster seen at thresholded map *dpv_tstat.mgz ?  This should correspond to
> your -log10(p) of your cluster.
>
> I personally did not use -logp and use the mri_surfcluster for the
> reporting of the clusters, as I wrote in previous mail here:
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html
>
> But it is only matter of personal preference.
>
> And, beware, that the LGI is very smooth measure, therefore also rather
> big cluster can be insignificant after FWER correction.
>
> Antonin
>
>
>
>
> Hi Antonin,
>
> Here, I am sending you more information:
>
> (1). I used following command:
> palm -i lh.Behav_LGI.10.mgh -s fsaverage/surf/lh.white
> fsaverage/surf/lh.white.avg.area.mgh -d Xg_Behav.csv -t
> Contrast_Behav.csv
> -m lh.Behav_LGI.glmdir/mask.mgh -o Results_Left -Cstat extent -C 1.95
> -approx tail -n 500 -nouncorrected -logp
>
> (2). Somehow, view of *_clustere_tstat_fwep is single colored, thresholded
> 0 (min) and 1(max), which seems suspicious. Please find it attached.
>
> (3). Data showed in screen shot 1 is just partial correlation coefficient
> (PCC, limiting between 0.30-0.35), obtained after running glm_fit command
> and saved in glm directory.
>
> (4). *_clustere_tstat_fwep is attached here in this email.
>
> (5). If I load *dpv_tstat.mgz and threshold it between 1.3 (p = 0.05) and
> 2
> (max), I get the map attached 2nd in attached figure. I am not sure
> how to "threshold
> it by your cluster-forming threshold (I suppose that you should correctly
> convert z value to t-value), to see your initial clusters after
> thresholding".
>
> Thanks a lot Antonin.
> Sahil
>
>
>
> On Wed, Mar 8, 2017 at 2:06 PM, Antonin Skoch  wrote:
>
> > Dear Sahil,
> >
> > could you send the full command-line and unthresholded view of
> > *_clustere_tstat_fwep ?
> >
> > How the data showed in screenshot 1 were produced?
> >
> > How are the actual p-values of your clusters in *_clustere_tstat_fwep?
> >
> > You can also use -saveglm and inspect the files containing values of GLM
> > fit.
> > You can load the *dpv_tstat.mgz file and threshold it by your
> > cluster-forming threshold (I suppose that you should correctly convert z
> > value to t-value), to see your initial clusters after thresholding.
> >
> > Regards,
> >
> > Antonin
> >
> >
> >
> > Thanks a lot Anderson and Antonin, that's really useful.
> >
> > Actually, I am having trouble in interpreting the results. Could you
> > please
> > share any document explaining all these tests/outputs and their
> > interpretation in simple terms?
> >
> > Here I am attaching a screen shot: (1) Simple partial correlations (I
> > adjusted the color bar between 0.30 and 0.35 to visualize the high
> > correlation coefficients, which is ~0.35) and (2) Results I get when I
> > used cluster
> > extent stats: *dpv_tstat
> > But I do not see any significant clusters when I view
> > *_clustere_tstat_fwep, *_dpv_tstat_fwep, which is very unexpected in my
> > data set.
> >
> > So basically I really doubt if I am running the stats correctly because
> > PCC
> > looks high at that big cluster (shown i

Re: [Freesurfer] Error viewing corrected results

[Sahil Bajaj]

 email.
> > > >
> > > > (5). If I load *dpv_tstat.mgz and threshold it between 1.3 (p =
> 0.05)
> > and
> > > > 2
> > > > (max), I get the map attached 2nd in attached figure. I am not sure
> > > > how to "threshold
> > > > it by your cluster-forming threshold (I suppose that you should
> > correctly
> > > > convert z value to t-value), to see your initial clusters after
> > > > thresholding".
> > > >
> > > > Thanks a lot Antonin.
> > > > Sahil
> > > >
> > > >
> > > >
> > > > On Wed, Mar 8, 2017 at 2:06 PM, Antonin Skoch  wrote:
> > > >
> > > > > Dear Sahil,
> > > > >
> > > > > could you send the full command-line and unthresholded view of
> > > > > *_clustere_tstat_fwep ?
> > > > >
> > > > > How the data showed in screenshot 1 were produced?
> > > > >
> > > > > How are the actual p-values of your clusters in
> > *_clustere_tstat_fwep?
> > > > >
> > > > > You can also use -saveglm and inspect the files containing values
> of
> > GLM
> > > > > fit.
> > > > > You can load the *dpv_tstat.mgz file and threshold it by your
> > > > > cluster-forming threshold (I suppose that you should correctly
> > convert z
> > > > > value to t-value), to see your initial clusters after
> thresholding.
> > > > >
> > > > > Regards,
> > > > >
> > > > > Antonin
> > > > >
> > > > >
> > > > >
> > > > > Thanks a lot Anderson and Antonin, that's really useful.
> > > > >
> > > > > Actually, I am having trouble in interpreting the results. Could
> you
> > > > > please
> > > > > share any document explaining all these tests/outputs and their
> > > > > interpretation in simple terms?
> > > > >
> > > > > Here I am attaching a screen shot: (1) Simple partial correlations
> > (I
> > > > > adjusted the color bar between 0.30 and 0.35 to visualize the high
> > > > > correlation coefficients, which is ~0.35) and (2) Results I get
> when
> > I
> > > > > used cluster
> > > > > extent stats: *dpv_tstat
> > > > > But I do not see any significant clusters when I view
> > > > > *_clustere_tstat_fwep, *_dpv_tstat_fwep, which is very unexpected
> in
> > my
> > > > > data set.
> > > > >
> > > > > So basically I really doubt if I am running the stats correctly
> > because
> > > > > PCC
> > > > > looks high at that big cluster (shown in PCC in attached screen
> > shot).
> > > > >
> > > > > Could you please suggest if there is any alternative (less
> stronger)
> > > > stat
> > > > > flag I can use here while running PALM command?
> > > > >
> > > > > I would be more than happy sharing any required files to interpret
> > the
> > > > > results.
> > > > >
> > > > > Thanks.
> > > > >
> > > > > On Wed, Mar 8, 2017 at 10:20 AM, Sahil Bajaj <
> sahil.br...@gmail.com>
> >
> > > > > wrote:
> > > > >
> > > > > > Thanks a lot Anderson and Antonin, that's really useful.
> > > > > >
> > > > > > Actually, I am having trouble in interpreting the results. Could
> > you
> > > > > > please share any document explaining all these tests/outputs and
> > their
> > > > > > interpretation in simple terms?
> > > > > >
> > > > > > Here I am attaching two screen shots: (1) Results I get when I
> > used
> > > > > cluster
> > > > > > extent stats: *dpv_tstat and (2). Simple partial correlations (I
> > > > > adjusted
> > > > > > the color bar between 0.30 and 0.35 to visualize the high
> > correlation
> > > > > > coefficients, which is ~0.35).
> > > > > > I do not see any significant clusters when I view
> > > > *_clustere_tstat_fwep,
> > > > > > *_dpv_tstat_fwep, which is very unexpected in my data set.
> > > > > >
> > > > > > So basically I really doubt if I am running the stats correctly
>

[Freesurfer] Contrast matrix for PVR

[Sahil Bajaj]

Hi everyone,

>From FreeSurfer manual and discussion forum, I found that volume and LGI
can be correlated using mri_glmfit command with -pvr flag.

For that, my fsgd file has age, gender as covariates and the file is as
following:

GroupDescriptorFile 1

Class Male

Class Female

Variables Age

Inputzerek1 Male 21

Input zerek2 Male 25

etc.

My concern is:

To run mri_glmfit command, I am not sure how to define my contrast matrix
if I am interested in removing the effect of age and sex.

1st option I tried is: 0 0.5 0.5 0 1

Here, I think first 0 regresses out age, 0.5 0.5 should be averaging over
males and females and last 0 1 correlates between volume and LGI. But this
looks like it is not giving me correct correlations maps, although there is
no error.

2nd option I tried is: 0 0 0 0 1

This looks like its working and maps look correct to me but I want to make
sure this is the correct contrast matrix and I am not sure how this matrix
is regressing out age and gender or 1st option is correct contrast matrix?

Thank you so much !

Best,

Sahil
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[Freesurfer] Eklund's 2016 and FreeSurfer

[Sahil Bajaj]

Hi,

I was wondering if there is any paper published by FreeSurfer team or
FreeSurfer experts (after Eklund's 2016 paper) stating that the cluster
failure issue is not an issue in FreeSurfer toolbox and/or whether CFT of
less than 0.05 or 0.01 to estimate cortical thickness/volume/area maps is
fine to use if Monte-Carlo simulations (MCZ) in FreeSurfer.

I am looking for any such paper to cite in one of my papers I am working
on.

Thanks !
Sahil
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Re: [Freesurfer] Eklund's 2016 and FreeSurfer

[Sahil Bajaj]

Thanks a lot Dr. Fischl.
I am looking forward to hearing back from Dr. Greve soon.

That's really exciting news that a paper addressing this issue (authored by
Dr. Greve and his team) will be out very soon.

Thanks for the updates !

Best,
Sahil

On Thu, Nov 23, 2017 at 8:15 AM, Bruce Fischl 
wrote:

> Hi Sahil
>
> Doug has a paper submitted on this topic and will probably respond soon,
> but give him a couple of days due to Thanksgiving
>
> cheers
> Bruce
>
>
> On Wed, 22 Nov 2017, Sahil Bajaj wrote:
>
> Hi,
>> I was wondering if there is any paper published by FreeSurfer team or
>> FreeSurfer experts (after Eklund's 2016 paper) stating that the cluster
>> failure issue is not an issue in FreeSurfer toolbox and/or whether CFT of
>> less than 0.05 or 0.01 to estimate cortical thickness/volume/area maps is
>> fine to use if Monte-Carlo simulations (MCZ) in FreeSurfer.
>>
>> I am looking for any such paper to cite in one of my papers I am working
>> on.
>>
>> Thanks !
>> Sahil
>>
>>
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[Freesurfer] Subjectwise extraction from ROIs

[Sahil Bajaj]

Hello experts,

I identified two clusters (X for thickness and Y for volume) showing
significant association between cortical measures (thickness and volume)
and motor-performance. I followed steps from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
and got several output files same as mentioned at the bottom of this page
i.e. cache*.*

I am interested in getting subject-wise thickness and volume values from
these two clusters X and Y.

>From previous posts, I found that these subjectwise cluster values (e.g.
thickness and volume) are saved in *.ocn.dat file. If that's correct, I
have following questions:

(1). When I look at *.ocn.dat file, subjectwise thickness values range
between 2-3 and volume values are in the range between 0-2. I am not sure
if that makes sense and what are the units of thickness and volume here?

(2). Since *.ocn.dat file for X gives subjectwise thickness value for
cluster X and *.ocn.dat file for Y gives subjectwise volume values for
cluster Y, so how can I get volume values for cluster X and thickness
values for cluster Y?

>From pervious FS discussion, I found that it can be done using *.ocn.annot
files e.g. to extract volume values from X, *.ocn.annot for X can be used
in mris_anatomical_stats file. To make sure and confirm that this is the
correct approach, I calculated thickness values for X using this approach,
expecting that these should match with *.ocn.dat for X but it's not
matching.
I also converted *.annot to *.label in native space following steps from
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html
but still values are not matching with *.ocn.dat.

I would really appreciate any help.

Thanks,
Sahil
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[Freesurfer] Fwd: Subjectwise extraction from ROIs

[Sahil Bajaj]

Hello everyone,

I was wondering if someone could please help me in figuring out following
issues.

Thanks a lot,
Sahil
-- Forwarded message --
From: Sahil Bajaj 
Date: Thu, Feb 15, 2018 at 3:50 PM
Subject: Subjectwise extraction from ROIs
To: Freesurfer support list 


Hello experts,

I identified two clusters (X for thickness and Y for volume) showing
significant association between cortical measures (thickness and volume)
and motor-performance. I followed steps from here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
and got several output files same as mentioned at the bottom of this page
i.e. cache*.*

I am interested in getting subject-wise thickness and volume values from
these two clusters X and Y.

>From previous posts, I found that these subjectwise cluster values (e.g.
thickness and volume) are saved in *.ocn.dat file. If that's correct, I
have following questions:

(1). When I look at *.ocn.dat file, subjectwise thickness values range
between 2-3 and volume values are in the range between 0-2. I am not sure
if that makes sense and what are the units of thickness and volume here?

(2). Since *.ocn.dat file for X gives subjectwise thickness value for
cluster X and *.ocn.dat file for Y gives subjectwise volume values for
cluster Y, so how can I get volume values for cluster X and thickness
values for cluster Y?

>From pervious FS discussion, I found that it can be done using *.ocn.annot
files e.g. to extract volume values from X, *.ocn.annot for X can be used
in mris_anatomical_stats file. To make sure and confirm that this is the
correct approach, I calculated thickness values for X using this approach,
expecting that these should match with *.ocn.dat for X but it's not
matching.
I also converted *.annot to *.label in native space following steps from
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg53591.html
but still values are not matching with *.ocn.dat.

I would really appreciate any help.

Thanks,
Sahil
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Re: [Freesurfer] Fwd: Subjectwise extraction from ROIs

[Sahil Bajaj]

Dear Dr. Greve,

I have following follow-up questions ('red' colored) for you and would
really appreciate any help.

On Tue, Feb 20, 2018 at 2:59 PM, Douglas N Greve 
wrote:

> sorry for the delay, thanks for reposting
>
>
> On 02/20/2018 11:33 AM, Sahil Bajaj wrote:
> > Hello everyone,
> >
> > I was wondering if someone could please help me in figuring out
> > following issues.
> >
> > Thanks a lot,
> > Sahil
> > -- Forwarded message --
> > From: *Sahil Bajaj* mailto:sahil.br...@gmail.com
> >>
> > Date: Thu, Feb 15, 2018 at 3:50 PM
> > Subject: Subjectwise extraction from ROIs
> > To: Freesurfer support list  > <mailto:freesurfer@nmr.mgh.harvard.edu>>
> >
> >
> > Hello experts,
> >
> > I identified two clusters (X for thickness and Y for volume) showing
> > significant association between cortical measures (thickness and
> > volume) and motor-performance. I followed steps from here:
> > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
> > <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>
> > and got several output files same as mentioned at the bottom of this
> > page i.e. cache*.*
> >
> > I am interested in getting subject-wise thickness and volume values
> > from these two clusters X and Y.
> >
> > From previous posts, I found that these subjectwise cluster values
> > (e.g. thickness and volume) are saved in *.ocn.dat file. If that's
> > correct, I have following questions:
> >
> > (1). When I look at *.ocn.dat file, subjectwise thickness values range
> > between 2-3 and volume values are in the range between 0-2. I am not
> > sure if that makes sense and what are the units of thickness and
> > volume here?
> Thickness is mm and the value is mean thickness, so that makes sense.
> Volume is mm3, and the value is "mean" volume, which makes less sense.
> You can multiply the mean volume by the number of vertices to get total
> volume.
>

Thanks for the clarification Dr. Greve. Could you please tell me how can I
find number of vertices for each cluster (subjectwise) so that I can
multiple that with mean volume values.

> >
> > (2). Since *.ocn.dat file for X gives subjectwise thickness value for
> > cluster X and *.ocn.dat file for Y gives subjectwise volume values for
> > cluster Y, so how can I get volume values for cluster X and thickness
> > values for cluster Y?
> Assuming that they are different cluster maps, you can run
> mri_segstats --seg thicknessglm/contrast/csdbase.sig.ocn.mgh --exclude 0
> --i  volumestack.mgh --avgwf volume.thickness-clusters.dat --sum
> deleteme.sum
> where volumestack would be the input to the volume-based glm.
>

Just to confirm volumestack is the file (lh.X_vol.10.mgh) generated after
following steps, correct?
mris_preproc --fsgd X.fsgd --target fsaverage --hemi lh --meas volume --out
X/lh.X_vol.mgh
mri_surf2surf --hemi lh --s fsaverage --sval X/lh.X_vol.mgh --fwhm 10
--cortex --tval X/lh.X_vol.10.mgh

Could you please confirm if that's correct?
If that's correct, then mri_segstats command as you described above gives
mean volume values again, so again I need number of vertices here and I am
not sure how to get number of vertices for corresponding clusters.

Thanks a lot.
Sahil


>
> > From pervious FS discussion, I found that it can be done using
> > *.ocn.annot files e.g. to extract volume values from X, *.ocn.annot
> > for X can be used in mris_anatomical_stats file. To make sure and
> > confirm that this is the correct approach, I calculated thickness
> > values for X using this approach, expecting that these should match
> > with *.ocn.dat for X but it's not matching.
> > I also converted *.annot to *.label in native space following steps
> > from
> > https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/
> msg53591.html
> > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu
> /msg53591.html>
> > but still values are not matching with *.ocn.dat.
> Use the mri_segstats command above
> >
> > I would really appreciate any help.
> >
> > Thanks,
> > Sahil
> >
> >
> >
> > ___
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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: https://gate.nmr.mgh.harvard.edu/fi

[Freesurfer] ICV bias in CV measures

[Sahil Bajaj]

External Email - Use Caution

Dear FS experts,

This paper was published in 2013:
https://www.sciencedirect.com/science/article/pii/S1053811913007064?via%3Dihub#s0040

I was just wondering if the current version of FreeSurfer can still
introduce bias in cortical volume measures if ICV is used as an covariate
or this has been fixed in the latest FS version.

Specific to this issue, if nothing has been updated in FS (since 2013),
would you still recommend to *ALWAYS* use ICV as a covariate while
comparing CV?

Thanks,
Sahil
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[Freesurfer] How to run GLM FIT simulation in parallel?

[Sahil Bajaj]

External Email - Use Caution

Hello experts,

I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm 1000 1.3 abs
--cwp 0.05 --2spaces command, but its taking forever even if I reduce # of
permutations from 1000 to 10.

I was just wondering if there’s a version of FreeSurfer for Slurm parallel
processing clusters.

Thanks !
Sahil
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Re: [Freesurfer] How to run GLM FIT simulation in parallel?

[Sahil Bajaj]

External Email - Use Caution

Dear Dr. Greve,

I have 45 subjects as input. SLURM is also a parallel processing pipeline
similar to PBS, Grid Engine, or Condor:
https://en.wikipedia.org/wiki/Slurm_Workload_Manager
I am not sure how can I speed up the mri_glmfit-sim processing.

Thanks !

On Thu, Dec 6, 2018 at 11:07 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I don't know what Slurm is, so I guess the answer is no. If you have
> multiple processors on your machine, you can use the --bg option. In
> general, I have not seen it take that long to run. How many input
> subjects do you have?
>
> On 12/06/2018 12:55 PM, Sahil Bajaj wrote:
> >
> > External Email - Use Caution
> >
> > Hello experts,
> >
> > I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm 1000 1.3
> > abs --cwp 0.05 --2spaces command, but its taking forever even if I
> > reduce # of permutations from 1000 to 10.
> >
> > I was just wondering if there’s a version of FreeSurfer for Slurm
> > parallel processing clusters.
> >
> > Thanks !
> > Sahil
> >
> >
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Re: [Freesurfer] How to run GLM FIT simulation in parallel?

[Sahil Bajaj]

External Email - Use Caution

Thanks Dr. Greve, actually I was using --bg 2 in my command line. Removing
--bg has now speeded up the process.

Thanks again for your help.

Regards,
Sahil

On Thu, Dec 6, 2018 at 12:04 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I think something is wrong if you only have 45 subjects, it should not
> take that long. Can you send your mri_glmfit command line and the
> terminal output of mri_glmfit-sim?
>
> On 12/06/2018 01:14 PM, Sahil Bajaj wrote:
> >
> > External Email - Use Caution
> >
> > Dear Dr. Greve,
> >
> > I have 45 subjects as input. SLURM is also a parallel processing
> > pipeline similar to PBS, Grid Engine, or Condor:
> > https://en.wikipedia.org/wiki/Slurm_Workload_Manager
> > I am not sure how can I speed up the mri_glmfit-sim processing.
> >
> > Thanks !
> >
> > On Thu, Dec 6, 2018 at 11:07 AM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > I don't know what Slurm is, so I guess the answer is no. If you have
> > multiple processors on your machine, you can use the --bg option. In
> >     general, I have not seen it take that long to run. How many input
> > subjects do you have?
> >
> > On 12/06/2018 12:55 PM, Sahil Bajaj wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hello experts,
> > >
> > > I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm
> > 1000 1.3
> > > abs --cwp 0.05 --2spaces command, but its taking forever even if I
> > > reduce # of permutations from 1000 to 10.
> > >
> > > I was just wondering if there’s a version of FreeSurfer for Slurm
> > > parallel processing clusters.
> > >
> > > Thanks !
> > > Sahil
> > >
> > >
> > > ___
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> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto:Freesurfer@nmr.mgh.harvard.edu>
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> >
> >
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> >
> >
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[Freesurfer] mri glm fit matrix is ill-conditioned

[Sahil Bajaj]

External Email - Use Caution

Hi experts,

I am running following command:


mri_glmfit.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd
PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf
fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir


Both FSGD and Contrast files are also attached.


After I run above command, I get following error (highlighted in red):


mri_glmfit --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd
PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf
fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

gdfRead(): reading PAI_SUI_ONLY_MILD_DEP2.fsgd

INFO: demeaning continuous variables

Continuous Variable Means (all subjects)

0 SUI 52. 2.11403

1 Age 32. 7.23332

2 DEP 55. 7.83786

Class Means of each Continuous Variable

1 Male  52.  32.  54.

2 Female  52.6667  32.1667  55.6667

INFO: gd2mtx_method is dods

Reading source surface
/data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/fsaverage/surf/lh.white

Number of vertices 163842

Number of faces327680

Total area 65416.984375

AvgVtxArea   0.399269

AvgVtxDist   0.721953

StdVtxDist   0.195470


$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

cwd /data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral

cmdline mri_glmfit.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd
PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf
fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

sysname  Linux

hostname hyperion

machine  x86_64

user scanlab

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y
/data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh

logyflag 0

usedti  0

FSGD PAI_SUI_ONLY_MILD_DEP2.fsgd

labelmask
/data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/fsaverage/label/lh.cortex.label

maskinv 0

glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

Loading y from
/data/emot/Freesurfer/FreeSurferSegmentation/SB_Behavioral/SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh

   ... done reading.

INFO: gd2mtx_method is dods

Saving design matrix to SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir/Xg.dat

Computing normalized matrix

Normalized matrix condition is 1e+08

Design matrix --

 0.0   1.0   0.0   1.68188   0.0  -0.01536   0.0
-1.67279;

 1.0   0.0  -0.68326   0.0   1.09063   0.0  -0.77969
0.0;

 0.0   1.0   0.0  -0.68326   0.0  -1.39785   0.0
2.02720;

 0.0   1.0   0.0  -0.68326   0.0   1.22888   0.0
-0.14176;

 1.0   0.0   0.73582   0.0  -0.29186   0.0   0.62375
0.0;

 1.0   0.0  -0.68326   0.0  -0.84486   0.0  -0.26935
0.0;

 0.0   1.0   0.0   1.68188   0.0  -1.12135   0.0
0.11341;

 0.0   1.0   0.0  -0.68326   0.0   1.50538   0.0
-0.65211;

 0.0   1.0   0.0  -0.68326   0.0  -0.15361   0.0
0.75134;



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.bin --y SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol.8.mgh --fsgd
PAI_SUI_ONLY_MILD_DEP2.fsgd dods --C Corr-PAI-SUI_ONLY_DEP.mtx --surf
fsaverage lh --cortex --glmdir SB_SUI_ONLY_MILD_DEP2/lh.SUI_vol8.glmdir

  2. The FSGD file (if using one)

  3. And the design matrix above

Attempting to diagnose further

SumSq: Min=1.034183 (col 7), Max=2.816108 (col 8)

 ... could not determine the cause of the problem


Both fsgd and contrast files are created in LINUX, and I also normalized my
data using DeMeanFlag 1

ReScaleFlag 1 as suggested here:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg49123.html


Could you please help in resolving this issue?


Thanks !

Sahil


Corr-PAI-SUI_ONLY_DEP.mtx
Description: Binary data


PAI_SUI_ONLY_MILD_DEP2.fsgd
Description: Binary data
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[Freesurfer] Unable to run recon all

[Sahil Bajaj]

External Email - Use Caution

Hello FS experts,

I am trying to run recon all on about 100 subjects. But one out of 100
subjects finishes recon all with error, and doesn't complete the process.
Here I am attaching recon all log for your reference. Also, before
installing freesurfer on MAC Catalina, I ran sudo spctl - -master -disable

I would really appreciate any help in resolving this.

Thanks,
Sahil

1) FreeSurfer version:

freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
2) Platform: MACOS Catalina
3) recon-all.log: see attached


recon-all.error
Description: Binary data
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Re: [Freesurfer] Unable to run recon all

[Sahil Bajaj]

External Email - Use Caution

Hi Dough,

I just uploaded one of the files on Martinos Center File Drop
<https://gate.nmr.mgh.harvard.edu/filedrop2/>. I hope that works !
(Somehow, uploading through ftp was taking too long).

Thanks.

On Mon, Jan 6, 2020 at 11:19 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> It is not clear why it failed for these subjects (always happens at the
> same place). Can you upload one of them for me to take a look at? here
> are the instructions
>
>  From the linux command line,
> Create the file you want to upload, eg,
> cd $SUBJECTS_DIR
> tar cvfz subject.tar.gz ./subject
> Now log  into our anonymous FTP site:
> ftp surfer.nmr.mgh.harvard.edu
> It will ask you for a user name: use "anonymous" (no quotes)
> It will ask you for a password: use "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
>
>
>
> On 1/6/20 11:49 AM, Sahil Bajaj wrote:
> >
> > External Email - Use Caution
> >
> > Hi Dough,
> >
> > I finished recon -all on about 515 subjects and I get error in 11 out
> > of 515 subjects. Here I am attaching recon-all.log files of all those
> > 11 subjects. I would really appreciate your help in fixing these errors.
> >
> > Thanks,
> > Sahil
> >
> > On Thu, Jan 2, 2020 at 10:03 AM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Can you send the recon-all.log file? You sent the .error file
> >
> > On 12/20/2019 10:13 AM, Sahil Bajaj wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Hello FS experts,
> >>
> >> I am trying to run recon all on about 100 subjects. But one out
> >> of 100 subjects finishes recon all with error, and doesn't
> >> complete the process. Here I am attaching recon all log for your
> >> reference. Also, before installing freesurfer on MAC Catalina, I
> >> ran sudo spctl - -master -disable
> >>
> >> I would really appreciate any help in resolving this.
> >>
> >> Thanks,
> >> Sahil
> >> 1) FreeSurfer version:
> >>
> >> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
> >>
> >> 2) Platform: MACOS Catalina
> >> 3) recon-all.log: see attached
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu   Freesurfer@nmr.mgh.harvard.edu>
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
> > 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.
>
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Re: [Freesurfer] Unable to run recon all

[Sahil Bajaj]

External Email - Use Caution

Hi Dough,

I was just wondering if you got a chance to look at the files I
uploaded on Martinos
Center File Drop <https://gate.nmr.mgh.harvard.edu/filedrop2/>. I would
really appreciate any help/updates.

Best,
Sahil

On Mon, Jan 6, 2020 at 11:50 AM Sahil Bajaj  wrote:

> Hi Dough,
>
> I just uploaded one of the files on Martinos Center File Drop
> <https://gate.nmr.mgh.harvard.edu/filedrop2/>. I hope that works !
> (Somehow, uploading through ftp was taking too long).
>
> Thanks.
>
> On Mon, Jan 6, 2020 at 11:19 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> It is not clear why it failed for these subjects (always happens at the
>> same place). Can you upload one of them for me to take a look at? here
>> are the instructions
>>
>>  From the linux command line,
>> Create the file you want to upload, eg,
>> cd $SUBJECTS_DIR
>> tar cvfz subject.tar.gz ./subject
>> Now log  into our anonymous FTP site:
>> ftp surfer.nmr.mgh.harvard.edu
>> It will ask you for a user name: use "anonymous" (no quotes)
>> It will ask you for a password: use "anonymous" (no quotes)
>> cd transfer/incoming
>> binary
>> put subject.tar.gz
>> Send an email that the file has been and the name of the file.
>>
>>
>>
>> On 1/6/20 11:49 AM, Sahil Bajaj wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hi Dough,
>> >
>> > I finished recon -all on about 515 subjects and I get error in 11 out
>> > of 515 subjects. Here I am attaching recon-all.log files of all those
>> > 11 subjects. I would really appreciate your help in fixing these errors.
>> >
>> > Thanks,
>> > Sahil
>> >
>> > On Thu, Jan 2, 2020 at 10:03 AM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > Can you send the recon-all.log file? You sent the .error file
>> >
>> > On 12/20/2019 10:13 AM, Sahil Bajaj wrote:
>> >>
>> >> External Email - Use Caution
>> >>
>> >> Hello FS experts,
>> >>
>> >> I am trying to run recon all on about 100 subjects. But one out
>> >> of 100 subjects finishes recon all with error, and doesn't
>> >> complete the process. Here I am attaching recon all log for your
>> >> reference. Also, before installing freesurfer on MAC Catalina, I
>> >> ran sudo spctl - -master -disable
>> >>
>> >> I would really appreciate any help in resolving this.
>> >>
>> >> Thanks,
>> >> Sahil
>> >> 1) FreeSurfer version:
>> >>
>> >> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>> >>
>> >> 2) Platform: MACOS Catalina
>> >> 3) recon-all.log: see attached
>> >>
>> >> ___
>> >> Freesurfer mailing list
>> >> Freesurfer@nmr.mgh.harvard.edu  > Freesurfer@nmr.mgh.harvard.edu>
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> > ___
>> > 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.
>>
>
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[Freesurfer] CORONA Research study in India - an online survey !

[Sahil Bajaj]

External Email - Use Caution

Dear all,

Our research group is looking for participants (age 19 years or older) who
are currently staying in India amid 21-days COVID-19 lock down, and can
complete an online 15 min survey about human behavior related to COVID-19.
If you meet these two eligibility conditions: (i) age 19 years or older,
and (ii) you are/were staying in India during 21-days lock-down period due
to CORONA virus, and are interested in participating in the study, please
email me back at sahil.br...@gmail.com to get the survey link.
Details about my research:
https://www.boystownhospital.org/research/faculty/sahil-bajaj

Given the seriousness of the disease, I would really appreciate if you can
contribute to scientific research related to COVID-19.

Thanks a lot !

Best, Sahil
-- 

-

*Sahil** Bajaj, Ph.D.*

Director, Multimodal Clinical Neuroimaging Laboratory (MCNL)

Center for Neurobehavioral Research

*E-mail:* sahil.ba...@boystown.org | *p:* 531.355.1053 | *f:* 531.355.1213


Boys Town National
*ResearchHospital*
Boys Town, NE 68010
Twitter <https://twitter.com/BoysTown> | LinkedIn
<https://www.linkedin.com/company/boys-town-national-research-hospital/>
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[Freesurfer] Job opportunity (ResearchAssistant/Lab Manager) at Boys Town National Research Hospital

[Sahil Bajaj]

External Email - Use Caution

*Business:* Boys Town National Research Hospital

*Job Summary:*

As a Research Assistant/Lab Manager of the Center for Neurobehavioral
Research (CNR), you join us in our work understanding the neurobiological
bases of adolescent externalizing and internalizing conditions. In this
role, you will be an integral member of the scientific team and will have
rich opportunities to participate in and learn from the Neurobehavioral
Development Study and multiple other neurodevelopmental studies from across
the CNR.

The CNR and Boys Town National Research Hospital provide an ideal training
environment for research assistants with extensive opportunities to learn
about clinical practice and fMRI.



Review of applications will begin as soon as they are received and will
continue until the position is filled.  Anticipated start date is July to
August 2021.

*Schedule*: Full-Time, 40 hours a week

*Responsibilities:*

   - Ensures that all laboratory materials, supplies, and equipment are
   ordered and available.
   - Performs or assists in the recruitment of research participants,
   including patients. Collaborates with laboratory PI to understand their
   recruiting needs.
   - Performs or assists in testing of research subjects.
   - Maintains detailed records of test conditions and results.
   - Manages purchasing of equipment and financial details (e.g. subject
   payment, petty cash, and mileage reimbursements).
   - Regularly enters data into lab databases and ensures scoring and data
   accuracy.

*Required Qualifications:*

   - Requires a BSc/BA degree directly related to the work involved in the
   research program (i.e., Psychology or Neuroscience).
   - Experience in Mental Health or other forms of psychological research,
   preferred
   - Job requires interpersonal skills, close attention to detail, and
   flexibility in duties performed.



About us: The Center for Neurobehavioral Research was established in 2016
to help improve the care of children through a better understanding of the
neurobiology of mental health. With a new, dedicated and state-of-the-art 3
Tesla scanner as well as fNIRS capability, the CNR assesses approximately
300 adolescents and a comparable number of young children annually on a
large neuroimaging battery, including tasks indexing emotion processing,
decision-making and response control, to determine dysfunction in specific
neuro-cognitive systems that underpin different forms of impaired mental
health. In addition to in-home family services and residential treatment
centers, Boys Town provides the Family Home ProgramSM, a treatment
foster-case program serving over 400 youth annually on the Boys Town campus
in Omaha, Nebraska.  Youth participating in the Family Home ProgramSM are
scanned before and after treatment completion to determine treatment
response. The CNR is also involved in the assessments of other
interventions – both pharmacological and psychosocial. The CNR therefore
offers a unique opportunity to study mechanisms underlying mental health
issues in large samples, with a translational focus. The CNR provides a
vigorous and highly collaborative research environment in which
post-doctoral fellows participate in team-based projects.



*For any questions/queries, please contact:*

*Sahil Bajaj, PhD*

Director Multimodal Clinical Neuroimaging Laboratory (MCNL)

E-mail: sahil.ba...@boystown.org

*&*

*James Blair, PhD*

Director, Center for Neurobehavioral Research

E-mail: james.bl...@boystown.org


*About Boys Town:*

Boys Town has been changing the way America cares for children and families
since 1917. With over a century of service, our employees have helped us
grow from a small boarding house in downtown Omaha, Nebraska, into one of
the largest national child and family care organizations in the country.
With the addition of Boys Town National Research Hospital in 1977, our
services branched out into the health care and research fields, offering
even more career opportunities to those looking to make a real difference.

Our employees are our #1 supporters when it comes to achieving Boys Town's
mission, which is why we are proud of their commitment to making the world
a better place for children, families, patients, and communities. Unique
perks to Boys Town employees and their families include free visits to Boys
Town physicians and free prescriptions under the Boys Town Medical Plan,
tuition assistance, parenting resources from our experts and professional
development opportunities within the organization, just to name a few.
Working at Boys Town is more than just a job, it is a way of life.

*Boys Town National Research Hospital is a tobacco free campus.  * *This
advertisement describes the general nature of work to be performed and does
not include an exhaustive list of all duties, skills, or abilities
required. Boys Town is an equal employment opportunity employer and
participates in the E-Verify pro

[Freesurfer] FreeView issue!

[Sahil Bajaj]

External Email - Use Caution

Hi everyone,

I am having following error while opening freeview in terminal:

BT136080:01_Project_FreeSurfer bajsah$ freeview -f
fsaverage/surf/lh.inflated

/Applications/freesurfer/7.1.1/bin/freeview: line 2: 27046 Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"


Somehow, this was working fine a few weeks ago, but I can't open freeview
now. I double checked the folder: /Applications/freesurfer/7.1.1/bin/freeview
and everything seems to be at place.


Any suggestions/tips to resolve this, please?


Thanks a lot !
Sahil
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Re: [Freesurfer] FreeView issue!

[Sahil Bajaj]

External Email - Use Caution

Hi Ruopeng

Thanks for your quick response.

If I use that I still get the similar error:

BT136080:~ bajsah$ $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
Segmentation fault: 11Segmentation fault: 11

Sahil

On Fri, Jul 16, 2021 at 1:23 PM Wang, Ruopeng 
wrote:

> What if you run:
>
> $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview -f
> fsaverage/surf/lh.inflated
>
> > On Jul 16, 2021, at 1:07 PM, Sahil Bajaj  wrote:
> >
> > External Email - Use Caution
> >
> >
> > Hi everyone,
> >
> > I am having following error while opening freeview in terminal:
> >
> > BT136080:01_Project_FreeSurfer bajsah$ freeview -f
> fsaverage/surf/lh.inflated
> > /Applications/freesurfer/7.1.1/bin/freeview: line 2: 27046 Segmentation
> fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
> >
> > Somehow, this was working fine a few weeks ago, but I can't open
> freeview now. I double checked the folder:
> /Applications/freesurfer/7.1.1/bin/freeview and everything seems to be at
> place.
> >
> > Any suggestions/tips to resolve this, please?
> >
> > Thanks a lot !
> > Sahil
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://secure-web.cisco.com/13WhlfKwyrHqlVUA6osOdxPEvEQqYk1_F4PsnJ0IFp8XnMKP1VFcQw77VW4deciVatD4-aBj_Yydg0fl54pdnWdygQQhJv_vYRkxSYu4BOs3bBg56WO5V3mpZLrp9vMNJugqLQAP_b4SaPujlU5QR63BiyTvTxTyUchSlneHJjwH72ncCNyhlUddWOFEfmjjFbKWNpCFq_e32JZlnaVyo6gTTpwSQsykZPjtNayvtfGpKyHc7vGJLXeBiicHQ-1cwMW0loXTxnWh8nNG2uwmQaQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/13WhlfKwyrHqlVUA6osOdxPEvEQqYk1_F4PsnJ0IFp8XnMKP1VFcQw77VW4deciVatD4-aBj_Yydg0fl54pdnWdygQQhJv_vYRkxSYu4BOs3bBg56WO5V3mpZLrp9vMNJugqLQAP_b4SaPujlU5QR63BiyTvTxTyUchSlneHJjwH72ncCNyhlUddWOFEfmjjFbKWNpCFq_e32JZlnaVyo6gTTpwSQsykZPjtNayvtfGpKyHc7vGJLXeBiicHQ-1cwMW0loXTxnWh8nNG2uwmQaQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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 Mass General
> Brigham Compliance HelpLine at
> http://secure-web.cisco.com/1TqPwBRuzQgPyALBCryaJ5RR3Qd9hLPEOxhly8GjffVWk6H9Als6hkXR4z5LkjIweYh7yVjK2NtyoOD13vwx6gM1oNN6NI7tAmyqBsOBEqMhCMFI2B5e8xckcpuxRMlqE_X7JPjEWEdWjSwOS8V9X5rC3OzheXb0VkNESxjhlk1JNbHFg8KPE8WnimRubC37nAIV12akFRoSV7UmaX_XnBmrQPV_zTY3RTHBb-N1PTfNW5JmpNT3_WCtkUi926kH3GpOOzClVaIwrae4-fhL1MA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  . 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.
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
>
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Re: [Freesurfer] FreeView issue!

[Sahil Bajaj]

External Email - Use Caution

Hi,

I reinstalled FreeSurfer and now the latest version i.e., 7.2.0, but
somehow I am still getting the same error message, please see below. I am
still unsure how can I fix this issue?

Last login: Wed Jul 21 12:43:52 on ttys003

 freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer/7.2.0

FSFAST_HOME   /Applications/freesurfer/7.2.0/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/7.2.0/subjects

MNI_DIR   /Applications/freesurfer/7.2.0/mni

FSL_DIR   /usr/local/fsl


The default interactive shell is now zsh.

To update your account to use zsh, please run `chsh -s /bin/zsh`.

For more details, please visit 
https://secure-web.cisco.com/1NayViq948wI2yc5kOEBSjlYK5Yuaj55DlGmUeAwVLjh0SOnYolzcsDDzFjElrcTSCPI-IaIAPpsbwB0s-bYXnq99HUpLfsLvOZE6U7BQs-Kh4MH81jn_4rG_u3nhhMS2CRiNDob1u5QrNOelD1g9JnANo-5sDH57hqOLAR2pWxqfUVVraFB9qJblNa8-8owff42fyWher7Cx8Q8B2GKv3yOqtM2RMI2MGOCzbzRhfrmiTSUBbTmYX4tx33ZuLbR-q1URO--snaUaYixEXh-1zQ/https%3A%2F%2Fsupport.apple.com%2Fkb%2FHT208050.

BT136080:~ bajsah$ export
FS_LICENSE=/Applications/freesurfer/7.2.0/license.txt

BT136080:~ bajsah$ ls -l $FS_LICENSE

-rw-r--r--@ 1 bajsah  FFBHNTS\Domain Users  58 Jul 21 12:34
/Applications/freesurfer/7.2.0/license.txt

BT136080:~ bajsah$ which freeview

/Applications/freesurfer/7.2.0/bin/freeview

BT136080:~ bajsah$ freeview

/Applications/freesurfer/7.2.0/bin/freeview: line 2: 19977 Segmentation
fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"

BT136080:~ bajsah$

On Tue, Jul 20, 2021 at 6:01 AM fsbuild  wrote:

> Your crash report listed an Intel Mac running BigSur 11.4.  The
> screenshot below shows running the freesurfer 7.2.0 release installed on an
> Intel Mac running BigSur 11.4 (after installing the pkg file from
> https://secure-web.cisco.com/1uAAvCdKWzVjf3-skvFQVJnuofl7-ctvviv3iwprsfxL19YZU1CH-LLyuYt-xiKotqw9g5WovPaqeuijYbf46QJLJC0zP6RkHk0Ee06ddctL90CjCxv7ZhO48WfcSaQiFPbFZbG0_6aqUlE3qRwo8K55JIcUDnB4IP3q4suMmKXjdE-vHHxNl7c0Z5aVg4O0krQ2ZWp5RirTOEFV86EFHKXMhSxVfXK2pe2393vbg2NrSSO9jIOOUS0lTianON_UYQtogdCsHFuRQ7Rd_y4-fGg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer-darwin-macOS-7.2.0.pkg).
>
>
> In the terminal window you will see FS_LICENSE was manually set in the
> environment to point to the license.txt file.  But the environment variable
> QT_MAC_WANTS_LAYER is not in the environment at all.  After opening an
> empty freeview window, the volume
> /Applications/freesurfer/7.2.0/subjects/bert/mri/brain.mgz was loaded.
> Please give that a try on your machine.
>
> - R.
>
>
>
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[Freesurfer] Job opportunity (ResearchAssistant) at Boys Town National Research Hospital

[Sahil Bajaj]

External Email - Use Caution

Please apply at
https://secure-web.cisco.com/1yo0ekSWIR0Yp45MZ3-6sWQmS9wHjqoQSAfI0CL1kuo7zD1QzqmlDkaj9B1kr2X90yA4Q58HRFrSjAkMk2UTjx1-Q5FXHVZ8WMP2pxkZZtOWtbs3lfjplX4AZzPzOWvEaQ5yy_5CEyALTIAWDE6mT6aJjbFoW-GQA-P0tXPfIHJHWOPwMJ27NuNxG-QXEhHYMbSlgoa1EVA0jVIa4lRYUObDHlfxprUTgzXxhT4qJ5vW5pENJfVBWLEDgRpO4ynVHBvQz0fZX-S8VYngS1bccN2PgHh_l9UZwE3FjNpSG-GdQ0NlWZvHn-2sGYC-_GN8c-nD5NqnlYPtql1TYZ2ugKw/https%3A%2F%2Fphg.tbe.taleo.net%2Fphg02%2Fats%2Fcareers%2Fv2%2FviewRequisition%3Forg%3DBOYSTOWN%26cws%3D54%26rid%3D18893

Job ID18893

GENERAL SUMMARY

Under the general supervision of appropriate Research Program Director or
of a Research Associate, works on various phases of research studies being
performed, including data entry and analysis, subject recruitment and
testing.
MAJOR RESPONSIBILITIES & DUTIES

   - Assists in data collection and managing databases. Will be responsible
   for entering data from testing, managing subject files and keeping track of
   subject compensation.
   - Assists in the recruitment, scheduling, and testing in research
   studies using human subjects. Will assist in advertising for new studies,
   phone screens of potential participants, scheduling testing and
   administering behavioral testing.
   - Uses computers to analyze results of experiments. Will assist in
   processing imaging data and collecting behavioral data for different
   research projects.
   - Utilizes Boys Town vehicle to complete requirements of the position.
   - Knowledge, Skills and Abilities Required
  - Ability to apply knowledge gained through coursework in psychology,
  biology, chemistry, physics, neuroscience and/or computer science.
  - Ability to operate a personal computer.
  - Ability to apply math aptitude in order to perform data analyses
  and generate results.
  - Ability to communicate well, both orally and in writing.

REQUIREMENTS OF THE JOB:

Bachelor's degree in psychology or neuroscience or related area or
equivalent

Previous research experience working with human subjects, preferred

Good interpersonal skills, close attention to details, math aptitude, and
flexibility in duties performed

Must possess a valid driver's license with a good driving record and pass
an annual Motor Vehicle Registration (MVR) check.



About Boys Town:  Boys Town has been changing the way America cares for
children and families since 1917. With over a century of service, our
employees have helped us grow from a small boarding house in downtown
Omaha, Nebraska, into one of the largest national child and family care
organizations in the country. With the addition of Boys Town National
Research Hospital in 1977, our services branched out into the health care
and research fields, offering even more career opportunities to those
looking to make a real difference.


Our employees are our #1 supporters when it comes to achieving Boys Town's
mission, which is why we are proud of their commitment to making the world
a better place for children, families, patients, and communities. Unique
perks to Boys Town employees and their families include free visits to Boys
Town physicians and free prescriptions under the Boys Town Medical Plan,
tuition assistance, parenting resources from our experts and professional
development opportunities within the organization, just to name a few.
Working at Boys Town is more than just a job, it is a way of life.

Date Posted: March 15, 20222

*Boys Town National Research Hospital is a tobacco free campus.*   This
advertisement describes the general nature of work to be performed and does
not include an exhaustive list of all duties, skills, or abilities
required. Boys Town is an equal employment opportunity employer and
participates in the E-Verify program. All qualified applicants will receive
consideration for employment without regard to race, color, religion, sex,
sexual orientation, gender identity and/or expression, national origin,
age, disability or veteran status. To request disability-related
accommodation in the application process, contact us at 1-877-639-6003.
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[Freesurfer] Faces and vertices error !

[Sahil Bajaj]

External Email - Use Caution

Hi FreeSurfer community,

I am trying to map subject-specific cortical thickness map to standard
fsaverage space and I ran the following command where sub1_filled is my
individual subject in native:

mri_surf2surf --srcsubject sub1_filled --srcsurfreg thickness --trgsubject
fsaverage --trgsurfreg thickness --hemi lh --sval sub1/surf/lh.thickness
--tval fsaverage/surf/lh.thickness


After I run the above command, I am getting the following output and error.
I am not sure how to resolve this and whether there is something wrong with
my command line or with the data. I would greatly appreciate any help.


Source registration surface changed to thickness

Target registration surface changed to thickness


7.4.1


setenv SUBJECTS_DIR /Users/sbajaj/FS_Projects/

cd /Users/sbajaj/FS_Projects

mri_surf2surf --srcsubject sub1_filled --srcsurfreg thickness --trgsubject
fsav1 --trgsurfreg thickness --hemi lh --sval sub1/surf/lh.thickness --tval
fsav1/surf/lh.thickness


sysname  Darwin

hostname MDACM0CL9004107

machine  x86_64

user sbajaj

srcsubject = sub1_filled

srcval = sub1/surf/lh.thickness

srctype=

trgsubject = fsav1

trgval = fsav1/surf/lh.thickness

trgtype=

srcsurfreg = thickness

trgsurfreg = thickness

srchemi= lh

trghemi= lh

frame  = 0

fwhm-in= 0

fwhm-out   = 0

label-src  = (null)

label-trg  = (null)

OKToRevFaceOrder  = 1

UseDualHemi = 0

Reading source surface reg
/Users/sbajaj/FS_Projects//sub1_filled/surf/lh.thickness

nquads=4456450,  nvertices=341

error: ERROR: MRISread: file
'/Users/sbajaj/FS_Projects//sub1_filled/surf/lh.thickness' has many more
faces than vertices!

Probably trying to use a scalar data file as a surface!
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Problem with FreeSurfer 8.0

[Sahil Bajaj]

External Email - Use Caution

Greetings,

I am trying to use the latest FreeSurfer version 8.0 (beta version) on my
Mac Book Pro. But somehow I am struggling to resolve the following issue
when I try to open FreeView.

When I checked the FreeSurfer directory - I can see that
/Applications/freesurfer/bin/freeview exists but
/Applications/freesurfer/Freeview.app/Contents/MacOS/freeview: does not
exist.

Any help would be greatly appreciated.

Best,
Sahil

sbajaj@XJ6RDJF6Y9 ~ % export FREESURFER_HOME=/Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.sh


 freesurfer-macOS-darwin_arm64-8.0.0-beta-20241103-b8aacdc 

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /Applications/freesurfer

FSFAST_HOME   /Applications/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR  /Applications/freesurfer/subjects

MNI_DIR   /Applications/freesurfer/mni

FSL_DIR   /Users/sbajaj/fsl

sbajaj@XJ6RDJF6Y9 ~ % freeview &

[1] 15056

 /Applications/freesurfer/bin/freeview: line 2:
/Applications/freesurfer/Freeview.app/Contents/MacOS/freeview: No such file
or directory
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.