[Freesurfer] Measuring total cortical volume

[Emelie Andersson]

Hello,

We have a some doubts about how to measure the total cortical volume. Is it
recommendable to use GM = pial surface - white matter?

Hope to hear from You,

Best regards
Emelie
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[Freesurfer] Repost: fsgd file

[Jacobs H (NP)]

Dear FreeSurfers,

I hope you can help me out with a problem in coding my fsgd file.
I want to examine the spatial difference between two cognitive measures on 
cortical thickness in one group.
Furthermore, I will correct for age (centered covariate).
So, I have 4 variables: group (class), 2 cognitive scores (continuous) and age 
(continuous).
How can I compare two continuous variables?
I have tried to list them as two variables in the fsgd (so not class):
e.g:
Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ age)
Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a 
surface sig file.
However, when I look at the scatterplot in tksurfer, I cannot see the two 
cognitive variables at the same time.
Is there a better way to do this?

Thanks a zillion times :)

Best wishes

Heidi




Dr. Heidi Jacobs
Postdoc researcher
Faculty of Health, Medicine and Life Sciences
School for Mental Health and Neurosciences
Division Cognitive Neuropsychiatry and Clinical Neurosciences
Alzheimer Center Limburg
h.jac...@maastrichtuniversity.nl
www.maastrichtuniversity.nl
www.heidijacobs.nl

Dr. Tanslaan 12, 6229 ET Maastricht
P.O. Box 616, 6200 MD Maastricht, The Netherlands
T +31 43 38 84 090 F +31 43 38 84 092


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[Freesurfer] Memory allocation problem trac-all -prior

[Rui Lavrador]

-- Forwarded message --
From: Rui Lavrador 
Date: 2012/7/16
Subject: Re: [Freesurfer] Memory allocation problem trac-all -prior
To: Anastasia Yendiki 


Hi Anastasia,
Each diffusion volume has 128x128x60 voxels, and there are 182138 voxels
inside of the brain mask.

Rui

2012/7/12 Anastasia Yendiki 

>
> Hi Rui - How many voxels are in your diffusion volume? How many of them
> are inside the mask?
>
> a.y
>
>
> On Thu, 12 Jul 2012, Rui Lavrador wrote:
>
>  Hi all,
>> I'm running tracula and when doing the step:
>> trac-all -prior -c single_subject
>>
>> After some time it gives this error:
>>
>> MRIalloc(218, 182, 182): could not allocate 158704 bytes for 49th slice
>>
>> Cannot allocate memory
>>
>> I' m running tracula on Ubuntu 10.04, with 4GB ram. The diffusion data is
>> DTI with 64 directions.
>>
>> This happens many times? I need more memory?
>>
>> Best regards,
>>
>> --
>> Rui Lavrador
>>
>>
>>
>>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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-- 
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Visual Neuroscience Laboratory
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Azinhaga de Santa Comba
3000-548 Coimbra, Portugal
Phone: +351 964985485
e-mail: rui.lavra...@fmed.uc.pt
e-mail2: ruilavra...@gmail.com




-- 
Rui Lavrador

Visual Neuroscience Laboratory
IBILI-Faculdade de Medicina
Azinhaga de Santa Comba
3000-548 Coimbra, Portugal
Phone: +351 964985485
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Re: [Freesurfer] parcellations to fmri space

[Douglas N Greve]

Hi Chris, I don't think there is such a tool. One thing you can do is to 
use the aparc+aseg.mgz as the source instead of the lh and rh surfaces 
separately. This might solve all of your problems.
doug


On 07/06/2012 12:02 PM, Christopher Bell wrote:
>
> Hello Freesurfers,
>
>
> I have developed a pipeline that uses mri_label2vol to take freesurfer 
> parcellations to
> native fmri space, and uses dilation (within mri_label2vol) to make 
> the ROIs larger since our resolution is only
> 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to 
> large voxel
> size and partial voluming wihout the dilation. However, since the lh 
> and rh are done
> separately by mri_label2vol, I now have overlap on the midline and 
> have to go through a bunch
> of masking steps to eliminate it.
>
> My question is; is there a tool that will take both lh/rh 
> parcellations to a new coordinate
> system, do dilation, and most importantly control for lh/rh overlap? 
> Or any other
> similar suggestions. Thanks!
>
> Basically I am looking to rework my pipeline, and it seems I should be 
> able
> to find a more parsimonious solution, than my "Rube Goldberg" approach.
>
> Chris
>
>
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Re: [Freesurfer] multiple correction

[Douglas N Greve]

On 07/06/2012 10:00 PM, Meng Li wrote:
> Hi, freesurfer expert,
> I performed the statistical analysis between two groups first in left 
> hemisphere, and got some regions which showed different.
> 1) so if I then do multiple correction, i don't need to run the 
> mri_glmfit-sim command, and just press the button of the monte carlo 
> null-z simulation in the qdec interface, am i right?
correct
> 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec 
> get the same results, or not?  and as to the option --cwpvalthresh, 
> should i choose 0.05 or 0.025?
If you are drawing conclusions from both hemispheres then you need to 
use .025
> 3) And what is the difference between fdr and mc-z correction?
mc-z uses a cluster-wise correction and controls the rate of false 
positive clusters. FDR is voxel-wise and controls the false discovery 
rate, which is the number of false positives relative to the total 
number of positives (as compared to the number of false positives 
relative to the total number of tests).

doug
> Thanks,
> Meng
>
>
>
>
>
>
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Re: [Freesurfer] qdec

[Douglas N Greve]

Hi Carolina, the FWHM is the "full-width/half-maximum" and indicates how 
much smoothing you have. This is surface-based smoothing, not volume 
based, and it can be difficult to compare to volume based smoothing as 
is done in fMRI. The surface-based smoothing can be larger because you 
don't have to worry about smoothing in white matter and CSF or jumping 
across a sulcus as you would at higher levels of volume-based smoothing. 
There is no answer to the actual level of smoothing you need because it 
depends on how big the blob is. 10mm is "typical". fMRI analysis often 
has this level of smoothing in the volum.e
doug

On 07/07/2012 02:44 PM, carolina.mr wrote:
> Hello,
> In the qdec analysis the default smoothing factor is 10. What does it 
> mean? For other technics such as fMRI we generally use a lower 
> smoothing factor (~3 or lower). What would happen if I low down the FWHM?
> Thank you, Carolina
>
>
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Fax: 617-726-7422

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Re: [Freesurfer] Ribbon

[Douglas N Greve]

You can try
mris_volmask \
 --label_left_white   2 --label_left_ribbon   3 \
 --label_right_white 41 --label_right_ribbon 42 \
 --save_ribbon $subjid

doug


On 07/08/2012 01:18 PM, Matt Glasser wrote:
> Hi Bruce,
>
> He just needs the grey matter part of a typical ribbon.mgz volume.  He lost
> some of his recon-all folder.
>
> Peace,
>
> Matt.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Sunday, July 08, 2012 12:17 PM
> To: Colin Reveley
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Ribbon
>
> Hi Colin
>
> what is the representation you want in the end? You can also fill the
> interior of the surfaces using mris_fill then do some boolean algebra on
> the results of e.g. the white and pial interiors.
>
> cheers
> Bruce
>
>
> On Sun, 8 Jul 2012, Colin Reveley wrote:
>
>> Hi - I need to make a ribbon volume. I have all the necessary surfaces,
> but
>> I'm lacking an aseg.mgz because the data is monkey. I saw one guy on the
>> list had success by just calling his orig.mgz aseg.mgz. I tried that, and
> it
>> calculated the left right pial and white distances. Men sadly it
> segfaulted.
>> The program mri_ribbon will give me separate left and white gm ribbons. I
>> combined those, coloured them 3 and 42 and did my level best to fill the
> wm
>> with the right values, but some bits are wrong.
>>
>> What I'm actually trying to do is use matt glassers myelin mapping in
> caret.
>> other things could be wrong than my ribbon estimate.
>>
>> If anyone has an idea how to make a good ribbon  without aseg I'd
> appreciate
>> it. Please bear in mind I may be missing much of what one gets when one
> runs
>> recon-all. I have thickness, curv, surfaces, filled.mgz, pretesselstion
>> wm.mgz not so much else. The filled.mgz doesn't fill all non cortex the
> way
>> the bert ribbon does, so it's not that useful.
>>
>> Thanks,
>>
>> Colin
>>
>>
>
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Fax: 617-726-7422

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Re: [Freesurfer] Bug in mri_segstats.c or MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c

[Douglas N Greve]

Hi Masaya, you are correct. I've put a new version here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
Can you test it out? It also fixes the partial volume computation problem.
thanks!
doug





On 07/06/2012 02:23 PM, Masaya Misaki wrote:
> I've posted a question about a strange behavior of mri_segstats if voxel size 
> isn't 1 mm3 and --pv
> option is used.
>
> I found a reason of this problem in the source code of mri_segstats.c
> (release_5_1_0 branch was checked out from read-only CVS source-code 
> repository)
>
> In mri_segstats.c the return value from 
> MRIvoxelsInLabelWithPartialVolumeEffects is used as the
> number of voxels;
>
> nhits =
> MRIvoxelsInLabelWithPartialVolumeEffects
> (seg, pvvol, StatSumTable[n].id, NULL, NULL);
> vol = nhits*voxelvolume;
>
> However, MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c returns 
> volume (e.g. volume +=
> vox_vol; or volume += vox_vol * pv;), not the number of voxels.
>
> nhits value is adjusted by voxel volume in mri_segstats.c (vol = 
> nhits*voxelvolume), so that the
> voxelvolume (vox_vol) is multiplied twice.
>
> The volume reported by mri_segstats, therefore, is too small if the voxel 
> volume is less than 1 mm^3
> or too large if the voxel volume is larger than 1 mm3.
>
> Note that this is not a problem when voxel volume is conformed to 1 mm3 
> (default option in recon-all).
>
> I think many of FreeSurfer programs do not support high-resolution (<  1mm3) 
> image without conforming
> to 1 mm3 voxel, but could you fix the problem of mri_segstats? I want to use 
> mri_segstats with
> partial volume correction for high-resolution MRI image.
>
> Thank you,
>
> --Masaya
>
>
> On 06/26/2012 08:40 AM, Masaya Misaki wrote:
>> Hello all,
>>
>> I found volume size reported by mri_segstats is changed very much
>> depending on voxel size when partial volume correction (--pv option) is
>> used. The difference was much larger than that can be explained by the
>> difference of image resolution.
>> (mri_segstats version is 1.75.22 2011/4/27 in FreeSurfer v5.1.0)
>>
>> When I performed segmentation for high-resolution image (voxel size = 0.5
>> mm^3), I found all volumes of segmented regions in aseg.stats was too
>> small; about 8 times smaller than that was estimated from 1mm^3 conformed
>> image.
>>
>> So I tested the effect of voxel size on mri_segstats.
>> At first, recon-all was run with conforming 1mm^3 voxel (default option).
>> Then aseg.mgz and norm.mgz were conformed to small voxel size, and
>> mri_segstats was applied to the conformed files:
>>
>> mri_convert aseg.mgz aseg_cs05.mgz -cs 0.5 ­rt nearest
>> mri_convert norm.mgz norm_cs05.mgz -cs 0.5
>> mri_segstats --seg aseg_cs05.mgz --pv norm_cs05.mgz \
>> --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \
>> --nonempty --excludeid 0 --sum aseg_cs05.stats
>>
>> (these are just for testing the effect of voxel size, not for actual
>> analysis)
>>
>> All volumes reported in aseg_cs05.stats (for 0.5mm^3 voxel) was about 8
>> times smaller than aseg.stats (for 1mm^3 voxel). So the reported volume
>> was scaled with the same ratio as the voxel size. Same effect was observed
>> when voxel size was conformed to larger one (e.g. 1.5mm^3); reported
>> volumes were about 3 times larger than those for 1mm^3-voxel. The number
>> of voxels in the segmented regions (Nvoxels column in aseg.stats) were
>> similar across different voxel sizes while voxel sizes are different.
>>
>> When --pv option was not used, the reported volumes were almost the same
>> across different voxel sizes. So the partial volume correction in
>> mri_segstats seems to depend on voxel size.
>>
>> Can I fix this with some missed options or shouldn't I use --pv option
>> for the image with voxel size other than 1mm^3?
>>
>> thanks,
>>
>>
>> --
>> Masaya Misaki Ph.D.
>>
>>
>
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Re: [Freesurfer] ROI from left to right hemi - cortical thickness

[Douglas N Greve]

Hi Irene, what are the instructions you are following? If you have 
mapped the lh.roi to the LH of the xhemi subject (making it the RH), 
then you can copy it to subject/label/rh.roi and run the normal stats.
doug

On 07/09/2012 04:31 AM, Irene Altarelli wrote:
> Dear all,
>
> I have a ROI on the left hemisphere and I'd like to extract cortical
> thickness values from the homologous region in the right hemisphere. For
> this I applied the interhemispheric registration process and got my ROI
> mapped into the right hemisphere in /subject/xhemi/label.
> However when I tried to run mris_anatomical_stats on /subject/xhemi it
> failed, as there is no wm.mgz file in /subject/xhemi/mri.
>
> Any suggestion would be greatly appreciated.
>
> Thank you,
> Irene
>
>
>
>

-- 
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Re: [Freesurfer] How to register FLAIR to T1?

[Douglas N Greve]

Often with FLAIR there is not enough gray-white contrast to run the 
registration. Try using the pial surface instead, with "-surf pial --t1" 
This tells it to use the pial surface as a boundary. The --t1 is needed 
because the intensity should go from bright to dark. Let me know if that 
does not fix the problem.
doug

On 07/10/2012 11:58 AM, Bruce Fischl wrote:
> glad to hear it :). You may need to repost (and possibly upload your
> data)
> On Tue, 10 Jul 2012, Ed Gronenschild wrote:
>
>> Hi Bruce,
>>
>> It is indeed from the same scan session.
>> I'll wait patiently, let Doug enjoy his vacation before
>> he gets bothered again by all our questions.
>>
>> Cheers,
>> Ed
>>
>> On 10 Jul 2012, at 16:57, Bruce Fischl wrote:
>>
>>> Hi Ed,
>>>
>>> sorry, you'll have to wait until Doug is back from vacation. Is this from
>>> the same session? I've always had it work on flair images using one of the
>>> types of initialization.
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Tue, 10 Jul 2012, Ed Gronenschild wrote:
>>>
 Hi Bruce,

 Unfortunately, this has no effect.

 Ed

 On 10 Jul 2012, at 16:40, Bruce Fischl wrote:

> Hi Ed
>
> you are using -t2, right? You can also try -init-header
>
> cheers
> Bruce
> On Tue, 10 Jul 2012,
> Ed Gronenschild wrote:
>
>> Hi Bruce,
>>
>> It is slightly better but still displacements
>> in all directions and rotations too exist.
>>
>> Ed
>>
>> On 10 Jul 2012, at 16:13, Bruce Fischl wrote:
>>
>>> try -init-spm
>>>
>>> cheers
>>> Bruce
>>> On Tue, 10 Jul 2012, Ed Gronenschild wrote:
>>>
 Hi,

 I would like to register FLAIR to T1.
 Specifications FLAIR:
 axial acquisition, 24 slices,
 pixel size = 0.45 * 0.45 mm^2
 slice thickness = 5.50 mm (no gap).

 The slices run from the top of the brain
 to just below the eyes. This is contrary
 to the T1 scan which covers the full head
 down to the neck.
 I have tried bbregiser as follows:

 bbregister --s 001 --mov 001_FLAIR.mgz \
 --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3

 and inspected the result with

 tkregister2 --mov 001_FLAIR.mgz \
 --reg 001_register.dat --surf

 The result looks bad, it is displaced and rotated
 by about 20 degrees with respect to T1.

 It makes hardly any difference if instead of --t1
 --t2 as contrast setting was used.

 Is there a better way to do this registration?
 For instance, should I crop T1 to about the
 same space as covered by FLAIR?

 (FreeSurfer v4.5.0, MacOSX 10.5)

 Cheers,
 Ed
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>>>
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>>> is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
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>>>
>>

>>
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Re: [Freesurfer] Measuring total cortical volume

[Douglas N Greve]

In the aseg.stats file, there will be these values

# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter 
volume, 218425.204942, mm^3
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter 
volume, 212261.052152, mm^3
# Measure Cortex, CortexVol, Total cortical gray matter volume, 
430686.257094, mm^3

does this work for you?
doug


On 07/16/2012 03:17 AM, Emelie Andersson wrote:
> Hello,
>
> We have a some doubts about how to measure the total cortical volume. 
> Is it recommendable to use GM = pial surface - white matter?
>
> Hope to hear from You,
>
> Best regards
> Emelie
>
>
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Re: [Freesurfer] Bug in mri_segstats.c or MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c

[Masaya Misaki]

Thanks Doug!
New version of mri_segstats is working fine for images with small voxels 
(<1mm3).

--Masaya

On 07/16/2012 09:43 AM, Douglas N Greve wrote:
> Hi Masaya, you are correct. I've put a new version here:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux
> Can you test it out? It also fixes the partial volume computation problem.
> thanks!
> doug
>
>
>
>
>
> On 07/06/2012 02:23 PM, Masaya Misaki wrote:
>> I've posted a question about a strange behavior of mri_segstats if voxel 
>> size isn't 1 mm3 and --pv
>> option is used.
>>
>> I found a reason of this problem in the source code of mri_segstats.c
>> (release_5_1_0 branch was checked out from read-only CVS source-code 
>> repository)
>>
>> In mri_segstats.c the return value from 
>> MRIvoxelsInLabelWithPartialVolumeEffects is used as the
>> number of voxels;
>>
>> nhits =
>>  MRIvoxelsInLabelWithPartialVolumeEffects
>>  (seg, pvvol, StatSumTable[n].id, NULL, NULL);
>> vol = nhits*voxelvolume;
>>
>> However, MRIvoxelsInLabelWithPartialVolumeEffects in utils/mri.c returns 
>> volume (e.g. volume +=
>> vox_vol; or volume += vox_vol * pv;), not the number of voxels.
>>
>> nhits value is adjusted by voxel volume in mri_segstats.c (vol = 
>> nhits*voxelvolume), so that the
>> voxelvolume (vox_vol) is multiplied twice.
>>
>> The volume reported by mri_segstats, therefore, is too small if the voxel 
>> volume is less than 1 mm^3
>> or too large if the voxel volume is larger than 1 mm3.
>>
>> Note that this is not a problem when voxel volume is conformed to 1 mm3 
>> (default option in recon-all).
>>
>> I think many of FreeSurfer programs do not support high-resolution (<  1mm3) 
>> image without conforming
>> to 1 mm3 voxel, but could you fix the problem of mri_segstats? I want to use 
>> mri_segstats with
>> partial volume correction for high-resolution MRI image.
>>
>> Thank you,
>>
>> --Masaya
>>
>>
>> On 06/26/2012 08:40 AM, Masaya Misaki wrote:
>>> Hello all,
>>>
>>> I found volume size reported by mri_segstats is changed very much
>>> depending on voxel size when partial volume correction (--pv option) is
>>> used. The difference was much larger than that can be explained by the
>>> difference of image resolution.
>>> (mri_segstats version is 1.75.22 2011/4/27 in FreeSurfer v5.1.0)
>>>
>>> When I performed segmentation for high-resolution image (voxel size = 0.5
>>> mm^3), I found all volumes of segmented regions in aseg.stats was too
>>> small; about 8 times smaller than that was estimated from 1mm^3 conformed
>>> image.
>>>
>>> So I tested the effect of voxel size on mri_segstats.
>>> At first, recon-all was run with conforming 1mm^3 voxel (default option).
>>> Then aseg.mgz and norm.mgz were conformed to small voxel size, and
>>> mri_segstats was applied to the conformed files:
>>>
>>> mri_convert aseg.mgz aseg_cs05.mgz -cs 0.5 ­rt nearest
>>> mri_convert norm.mgz norm_cs05.mgz -cs 0.5
>>> mri_segstats --seg aseg_cs05.mgz --pv norm_cs05.mgz \
>>>  --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \
>>>  --nonempty --excludeid 0 --sum aseg_cs05.stats
>>>
>>> (these are just for testing the effect of voxel size, not for actual
>>> analysis)
>>>
>>> All volumes reported in aseg_cs05.stats (for 0.5mm^3 voxel) was about 8
>>> times smaller than aseg.stats (for 1mm^3 voxel). So the reported volume
>>> was scaled with the same ratio as the voxel size. Same effect was observed
>>> when voxel size was conformed to larger one (e.g. 1.5mm^3); reported
>>> volumes were about 3 times larger than those for 1mm^3-voxel. The number
>>> of voxels in the segmented regions (Nvoxels column in aseg.stats) were
>>> similar across different voxel sizes while voxel sizes are different.
>>>
>>> When --pv option was not used, the reported volumes were almost the same
>>> across different voxel sizes. So the partial volume correction in
>>> mri_segstats seems to depend on voxel size.
>>>
>>> Can I fix this with some missed options or shouldn't I use --pv option
>>> for the image with voxel size other than 1mm^3?
>>>
>>> thanks,
>>>
>>>
>>> --
>>> Masaya Misaki Ph.D.
>>>
>>>
>>
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>>
>>
>


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Re: [Freesurfer] Repost: fsgd file

[Douglas N Greve]

Hi Heidi, how exactly do you want to draw a conclusion? The slopes for 
the different variables may be very different because the variables have 
a different scale. tksurfer scatter plot is made to look at a cortical 
variable vs a continuous variable. If you want to look at a scatter plot 
of your continuous variables, why not just do it in matlab or excel?
doug

On 07/16/2012 04:47 AM, Jacobs H (NP) wrote:
> Dear FreeSurfers,
>
> I hope you can help me out with a problem in coding my fsgd file.
> I want to examine the spatial difference between two cognitive measures on 
> cortical thickness in one group.
> Furthermore, I will correct for age (centered covariate).
> So, I have 4 variables: group (class), 2 cognitive scores (continuous) and 
> age (continuous).
> How can I compare two continuous variables?
> I have tried to list them as two variables in the fsgd (so not class):
> e.g:
> Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ 
> age)
> Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a 
> surface sig file.
> However, when I look at the scatterplot in tksurfer, I cannot see the two 
> cognitive variables at the same time.
> Is there a better way to do this?
>
> Thanks a zillion times :)
>
> Best wishes
>
> Heidi
>
>
>
> 
> Dr. Heidi Jacobs
> Postdoc researcher
> Faculty of Health, Medicine and Life Sciences
> School for Mental Health and Neurosciences
> Division Cognitive Neuropsychiatry and Clinical Neurosciences
> Alzheimer Center Limburg
> h.jac...@maastrichtuniversity.nl
> www.maastrichtuniversity.nl
> www.heidijacobs.nl
>
> Dr. Tanslaan 12, 6229 ET Maastricht
> P.O. Box 616, 6200 MD Maastricht, The Netherlands
> T +31 43 38 84 090 F +31 43 38 84 092
> 
>
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>
>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] Flip brain

[Douglas N Greve]

Hi Tadeu, I have updated the files. The only difference is that the 
"mcc" file below is now

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor.tar.gz
  


doug

On 07/10/2012 09:25 AM, Tadeu Kubo wrote:
> Hi Dear FS experts,
>
> Doug sent these links, but I can't download them. Do you have the new 
> links?
>
> Download these files
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfreg
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/xhemireg
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.tar.gz
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsaverage_sym.mcc.tar.gz
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.linux
>
> Thank you.
>
> Regards,
> Tadeu
>
>
>
>
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Re: [Freesurfer] qdec - ERROR: CSDread():

[Douglas N Greve]

Does 
/Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd
 
exist and do you have read permission?
doug

On 07/10/2012 09:20 AM, Natalia h wrote:
> Dear expert,
>
> I got an error while clicking the Monte Carlo simulation in qdec.
> I am using Mac 10.6 and qdec version 1.4, freesufer 5.1
>
> Have no clue why it always gives this error in the terminal:
>
> mri_surfcluster --in 
> /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/sig.mgh
>  
> --csd 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd
>  
> --mask /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/mask.mgh 
> --cwsig 
> /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.mgh
>  
> --vwsig 
> /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.vertex.mgh
>  
> --sum 
> /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.cluster.summary
>  
> --ocn 
> /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.mgh
>  
> --oannot 
> /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.sig.ocn.annot
>  
> --csdpdf 
> /Longitudinal_template2/qdec/lh-thick-rate-10mm-group/lh-Avg-Intercept-long.thickness-rate/mc-z.abs.th20.pdf.dat
>  
> --annot aparc --cwpvalthresh 0.05 --surf white
>
> ERROR: CSDread(): could not open 
> /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm9/abs/th20/mc-z.csd
>  
>
>
> ERROR!
>
>
> Very appreciate for the help !
>
> Thank you in advance,
>
> Natalia
>
>
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Re: [Freesurfer] mri_glmfit

[Douglas N Greve]

Hmmm, that is strange. It's the same error as my previous email. Can you 
verify that the file below exists and that you can read it?
/apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/pos/th20/mc-z.csd


On 07/12/2012 04:28 PM, Jenny Liu wrote:
> Hello
>
> I typed in the command for multiple comparison:
> $ mri_glmfit-sim --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir 
> --cwpvalthresh 0.05 --cache 2.0 pos
>
> It starts to process, but there is an error (see below). How do I fix 
> this?
> Thanks,
> Jenny
>
>
> mdline mri_glmfit --y 
> rh.tp1_mnp_ltm_age_T1.H.Unp.Int.thickness.10B.mgh --fsgd 
> tp1_mnp_ltm_age_T1.H.Unp.Int.fsgd dods --C pain_C1_group_diff.mtx --C 
> pain_C3_group_x_painint.mtx --C pain_C6_avg_painint.mtx --surf average 
> rh --cortex --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir
> SURFACE: average rh
> log file is 
> rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir/cache.mri_glmfit-sim.log
>
> cd /study4/NCCAM/Data/MRI/processed/structural/freesurfer
> /apps/x86_64_sci6/freesurfer-latest/bin/mri_glmfit-sim
> --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir --cwpvalthresh 0.05 
> --cache 2.0 pos
>
> $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $
> Thu Jul 12 15:24:55 CDT 2012
> Linux balsa.keck.waisman.wisc.edu  
> 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 09:58:09 CDT 2012 x86_64 
> x86_64 x86_64 GNU/Linux
> jliu
> setenv SUBJECTS_DIR /study/NCCAM/Data/MRI/processed/structural/freesurfer
> FREESURFER_HOME /apps/x86_64_sci6/freesurfer-latest
>
> Original mri_glmfit command line:
> cmdline mri_glmfit --y 
> rh.tp1_mnp_ltm_age_T1.H.Unp.Int.thickness.10B.mgh --fsgd 
> tp1_mnp_ltm_age_T1.H.Unp.Int.fsgd dods --C pain_C1_group_diff.mtx --C 
> pain_C3_group_x_painint.mtx --C pain_C6_avg_painint.mtx --surf average 
> rh --cortex --glmdir rh.tp1_mnp_ltm_age_T1.H.Unp.Int.glmdir
>
> DoSim = 0
> UseCache = 1
> DoPoll = 0
> DoPBSubmit = 0
> DoBackground = 0
> DiagCluster = 0
> gd2mtx = dods
> fwhm = 13.724818
> ERROR: cannot find 
> /apps/x86_64_sci6/freesurfer-latest/average/mult-comp-cor/average/rh/cortex/fwhm14/pos/th20/mc-z.csd
>
>
>
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[Freesurfer] Coordinate Transformations

[jmd33]

 

Hi, 

I'm working on a project project comparing the cortical
thickness in epileptic patients to the corresponding brain area of a
control subject. To do this, I have been trying to transform the patient
RAS coordinates to talairach coordinates and then transforming the
talairach coordinates into the RAS coordinates of the control. In doing
this, I have two problems. First, when I use the transformation matrix
provided in the free surfer subject folder (multiply RAS coordinate by
transformation matrix in /mri/transforms/talairach.xfm) the coordinates
seem to map to similar although not exactly the same area. Second, what
is the best way to transform a set a talairach coordinates to RAS
coordinates? 

Thank you for your help, 

Jared 
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Re: [Freesurfer] Repost: fsgd file

[Jacobs H (NP)]

Hi Doug,

Thanks for your reply.
Both scores are on the same scale (z-transformed). But I would like to see 
whether there is a differential effect on cortical thickness. 
Do you think the contrast I defined was correct? And do I understand it 
correctly that what you suggest is the following: warp the clusters to 
individual space and extract the values for SPSS (or excel)?

Thanks!
Heidi

Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Verzonden: maandag 16 juli 2012 18:17
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Repost: fsgd file

Hi Heidi, how exactly do you want to draw a conclusion? The slopes for
the different variables may be very different because the variables have
a different scale. tksurfer scatter plot is made to look at a cortical
variable vs a continuous variable. If you want to look at a scatter plot
of your continuous variables, why not just do it in matlab or excel?
doug

On 07/16/2012 04:47 AM, Jacobs H (NP) wrote:
> Dear FreeSurfers,
>
> I hope you can help me out with a problem in coding my fsgd file.
> I want to examine the spatial difference between two cognitive measures on 
> cortical thickness in one group.
> Furthermore, I will correct for age (centered covariate).
> So, I have 4 variables: group (class), 2 cognitive scores (continuous) and 
> age (continuous).
> How can I compare two continuous variables?
> I have tried to list them as two variables in the fsgd (so not class):
> e.g:
> Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ 
> age)
> Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a 
> surface sig file.
> However, when I look at the scatterplot in tksurfer, I cannot see the two 
> cognitive variables at the same time.
> Is there a better way to do this?
>
> Thanks a zillion times :)
>
> Best wishes
>
> Heidi
>
>
>
> 
> Dr. Heidi Jacobs
> Postdoc researcher
> Faculty of Health, Medicine and Life Sciences
> School for Mental Health and Neurosciences
> Division Cognitive Neuropsychiatry and Clinical Neurosciences
> Alzheimer Center Limburg
> h.jac...@maastrichtuniversity.nl
> www.maastrichtuniversity.nl
> www.heidijacobs.nl
>
> Dr. Tanslaan 12, 6229 ET Maastricht
> P.O. Box 616, 6200 MD Maastricht, The Netherlands
> T +31 43 38 84 090 F +31 43 38 84 092
> 
>
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>
>

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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] ROI from left to right hemi - cortical thickness

[Irene Altarelli]

Dear Doug,

thanks for your answer. I guess I got confused by the output of the
interhemispheric registration.

So, to be sure I understood correctly: are you suggesting that I should

1) run 
mri_label2label --srcsubject suj1 --trgsubject suj1/xhemi --srclabel
$SUBJECT_DIR/suj1/label/lh.mylabel.label --trglabel
$SUBJECT_DIR/suj1/xhemi/label/lh.mylabel.label --regmethod surface
--surfreg sphere --hemi lh

2) copy the newly created label /suj1/xhemi/label/lh.mylabel.label to
suj1/label/rh.mylabel.label and calculate stats from that one?

Thanks again!
Have a nice day,
Irene


Le lundi 16 juillet 2012 à 10:49 -0400, Douglas N Greve a écrit :
> Hi Irene, what are the instructions you are following? If you have 
> mapped the lh.roi to the LH of the xhemi subject (making it the RH), 
> then you can copy it to subject/label/rh.roi and run the normal stats.
> doug
> 
> On 07/09/2012 04:31 AM, Irene Altarelli wrote:
> > Dear all,
> >
> > I have a ROI on the left hemisphere and I'd like to extract cortical
> > thickness values from the homologous region in the right hemisphere. For
> > this I applied the interhemispheric registration process and got my ROI
> > mapped into the right hemisphere in /subject/xhemi/label.
> > However when I tried to run mris_anatomical_stats on /subject/xhemi it
> > failed, as there is no wm.mgz file in /subject/xhemi/mri.
> >
> > Any suggestion would be greatly appreciated.
> >
> > Thank you,
> > Irene
> >
> >
> >
> >
> 

-- 

Irene Altarelli
Laboratoire de Sciences Cognitives et Psycholinguistique 
Ecole Normale Supérieure
29, rue d'Ulm
75230 Paris Cedex 05
tel. +33 (0)1 44 32 26 23


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Re: [Freesurfer] ROI from left to right hemi - cortical thickness

[Douglas N Greve]

that looks right except "--surfreg sphere" should be "--surfreg 
fsaverage_sym.sphere.reg"
Where did you get those instructions? Did I send them out before?
doug

On 07/16/2012 01:32 PM, Irene Altarelli wrote:
> Dear Doug,
>
> thanks for your answer. I guess I got confused by the output of the
> interhemispheric registration.
>
> So, to be sure I understood correctly: are you suggesting that I should
>
> 1) run
> mri_label2label --srcsubject suj1 --trgsubject suj1/xhemi --srclabel
> $SUBJECT_DIR/suj1/label/lh.mylabel.label --trglabel
> $SUBJECT_DIR/suj1/xhemi/label/lh.mylabel.label --regmethod surface
> --surfreg sphere --hemi lh
>
> 2) copy the newly created label /suj1/xhemi/label/lh.mylabel.label to
> suj1/label/rh.mylabel.label and calculate stats from that one?
>
> Thanks again!
> Have a nice day,
> Irene
>
>
> Le lundi 16 juillet 2012 à 10:49 -0400, Douglas N Greve a écrit :
>> Hi Irene, what are the instructions you are following? If you have
>> mapped the lh.roi to the LH of the xhemi subject (making it the RH),
>> then you can copy it to subject/label/rh.roi and run the normal stats.
>> doug
>>
>> On 07/09/2012 04:31 AM, Irene Altarelli wrote:
>>> Dear all,
>>>
>>> I have a ROI on the left hemisphere and I'd like to extract cortical
>>> thickness values from the homologous region in the right hemisphere. For
>>> this I applied the interhemispheric registration process and got my ROI
>>> mapped into the right hemisphere in /subject/xhemi/label.
>>> However when I tried to run mris_anatomical_stats on /subject/xhemi it
>>> failed, as there is no wm.mgz file in /subject/xhemi/mri.
>>>
>>> Any suggestion would be greatly appreciated.
>>>
>>> Thank you,
>>> Irene
>>>
>>>
>>>
>>>

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Re: [Freesurfer] Coordinate Transformations

[Douglas N Greve]

Have you looked at this page 
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

doug

On 07/16/2012 12:43 PM, jmd33 wrote:
>
> Hi,
>
> I'm working on a project project comparing the cortical thickness in 
> epileptic patients to the corresponding brain area of a control 
> subject. To do this, I have been trying to transform the patient RAS 
> coordinates to talairach coordinates and then transforming the 
> talairach coordinates into the RAS coordinates of the control.  In 
> doing this, I have two problems. First, when I use the transformation 
> matrix provided in the free surfer subject folder (multiply RAS 
> coordinate by transformation matrix in /mri/transforms/talairach.xfm) 
> the coordinates seem to map to similar although not exactly the same 
> area.  Second, what is the best way to transform a set a talairach 
> coordinates to RAS coordinates?
>
> Thank you for your help,
>
> Jared
>
>
>
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Re: [Freesurfer] Repost: fsgd file

[Douglas N Greve]

That contrast is correct. If you run mri_glmfit-sim, it will extract the 
data for each subject and cluster and save it in a text file in the 
contrast directory. It is better to do it this way instead of mapping 
the ROIs back to the individual. Look at mri_glmfit-sim --help
doug

On 07/16/2012 12:52 PM, Jacobs H (NP) wrote:
> Hi Doug,
>
> Thanks for your reply.
> Both scores are on the same scale (z-transformed). But I would like to see 
> whether there is a differential effect on cortical thickness.
> Do you think the contrast I defined was correct? And do I understand it 
> correctly that what you suggest is the following: warp the clusters to 
> individual space and extract the values for SPSS (or excel)?
>
> Thanks!
> Heidi
> 
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Verzonden: maandag 16 juli 2012 18:17
> Aan: freesurfer@nmr.mgh.harvard.edu
> Onderwerp: Re: [Freesurfer] Repost: fsgd file
>
> Hi Heidi, how exactly do you want to draw a conclusion? The slopes for
> the different variables may be very different because the variables have
> a different scale. tksurfer scatter plot is made to look at a cortical
> variable vs a continuous variable. If you want to look at a scatter plot
> of your continuous variables, why not just do it in matlab or excel?
> doug
>
> On 07/16/2012 04:47 AM, Jacobs H (NP) wrote:
>> Dear FreeSurfers,
>>
>> I hope you can help me out with a problem in coding my fsgd file.
>> I want to examine the spatial difference between two cognitive measures on 
>> cortical thickness in one group.
>> Furthermore, I will correct for age (centered covariate).
>> So, I have 4 variables: group (class), 2 cognitive scores (continuous) and 
>> age (continuous).
>> How can I compare two continuous variables?
>> I have tried to list them as two variables in the fsgd (so not class):
>> e.g:
>> Input101 group 2.3 1.9 -0.5 (number of subject / group / score 1/ score 2/ 
>> age)
>> Then I ran the dods model with the contrast 0 -1 1 0, which ended up with a 
>> surface sig file.
>> However, when I look at the scatterplot in tksurfer, I cannot see the two 
>> cognitive variables at the same time.
>> Is there a better way to do this?
>>
>> Thanks a zillion times :)
>>
>> Best wishes
>>
>> Heidi
>>
>>
>>
>> 
>> Dr. Heidi Jacobs
>> Postdoc researcher
>> Faculty of Health, Medicine and Life Sciences
>> School for Mental Health and Neurosciences
>> Division Cognitive Neuropsychiatry and Clinical Neurosciences
>> Alzheimer Center Limburg
>> h.jac...@maastrichtuniversity.nl
>> www.maastrichtuniversity.nl
>> www.heidijacobs.nl
>>
>> Dr. Tanslaan 12, 6229 ET Maastricht
>> P.O. Box 616, 6200 MD Maastricht, The Netherlands
>> T +31 43 38 84 090 F +31 43 38 84 092
>> 
>>
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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
>
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Re: [Freesurfer] annot 2 label file conversion

[Douglas N Greve]

Can you send your command line and the full terminal output?
doug

On 07/11/2012 09:39 AM, Bruce Fischl wrote:
> Hi Arnaud
>
> this question may need to wait for Doug to return. If you don't get an 
> answer in a couple of days try reposting, and please include your 
> exact command line and screen output and FS version.
>
> cheers
> Bruce
>
> On Wed, 11 Jul 2012, Arnaud Messé wrote:
>
>> Hi there,
>> I've some troubles with parcellisation schemes.
>> I've used mri_annotation2label to extract labels within annot file.
>> When I read the annot file within matlab (read_annotation.m), I found
>> 869 entries, everything looks good so far.
>> However, when I look at the output directory of labels, I only found 770
>> label file. For another parcellisation scheme, I found 325 entries in
>> annot file and 496 label files... These findings are consistent across
>> several subjects.
>> So my question is how mri_annotation2label processes annot file? and how
>> to find correspondence between annot and label files?
>> Any advice would be greatly appreciate,
>>
>>
>>
>
>
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Re: [Freesurfer] Clusterwise correction for multiple comparisons

[Douglas N Greve]

It does not seem like it should take that much time. You might try this 
program 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_mcsim.linux

This is what I use to create the cached results that we distribute. You 
can use the cached results unless you have a different mask. If you use 
mri_mcsim, there will be a few extra steps (not just a replacement for 
mri_glmfit-sim). Let me know if you get that far.
doug


On 07/11/2012 06:50 AM, Ed Gronenschild wrote:
> Hi,
>
> I'm performing a clusterwise correction for multiple comparisons
> with the command
>
> mri_glmfit-sim --glmdir my_glmdir --sim mc-z 5000 1.3 basename \
> --sim-sign abs
>
> For version v4.5.0 this took about 40 hours to complete.
> However, for v5.1.0 it is now running for more than
> 6 days and from the csd file I can read that it still has more
> than 1000 steps to go. Is it possible that it takes that
> much time?
>
> Cheers,
> Ed
>
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Re: [Freesurfer] ROI functional & anatomical cross

[Douglas N Greve]

You can create a binary mask of the ROI, then use mri_mask to mask out 
the non-ROI part from the fMRI. does that work?
doug

On 07/11/2012 11:25 AM, Huiting Liu wrote:
>
> Hello,
>
>
> I'm trying to do an ROI analysis that crosses the group-level 
> functional activation with specific anatomical structures. Currently 
> the clusters found for our group-level functional activation are too 
> large and need to be separated into many structures. Is there a 
> command I could use that would cross the group level map with each 
> cortical structure generated by freesurfer's recon-all?
>
>
> Thanks.
>
>
>
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Re: [Freesurfer] the make_average_subject without aparc.annot

[Douglas N Greve]

I don't remember what I sent out before, but you can try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
doug


On 07/11/2012 03:37 PM, Leon wrote:
> Hi, Doug
>
> I found from the archive that you made a version of 
> make_average_surface without the need for aparc.annot. I tried to 
> download it but the link is not valid anymore. Could you please send 
> me a copy of the file? I need to generate an averaged surface for a 
> group of non-human primates and I was asked to input these annotation 
> files that do not exist for non-human primate data.
>
> Many thanks!
> Leon
>
>
> Re: [Freesurfer] how to generate aparc.annotion files?
>
> Douglas N Greve
> Mon, 08 Nov 2010 09:55:49 -0800
>
> It is needed in make_average_surface. I've created a new version that
> does not use the aparc (thought I have not tested it). You can get it
> from here:
>
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc
>
> Make a backup of your current version of make_average_surface and then
> copy this one over it
>
> douig

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Re: [Freesurfer] parcellations to fmri space

[Christopher Bell]

I tried using mri_label2vol with --aparc+aseg instead of --aparc. This
works and provides cortical and subcortical with no overlap. It doesn't
allow me to do cortical dilation, but that is probably because it wouldn't
mesh
well with the subcortical ROIs. Thanks.

Chris


On Mon, Jul 16, 2012 at 9:03 AM, Douglas N Greve
wrote:

>
> Hi Chris, I don't think there is such a tool. One thing you can do is to
> use the aparc+aseg.mgz as the source instead of the lh and rh surfaces
> separately. This might solve all of your problems.
> doug
>
>
> On 07/06/2012 12:02 PM, Christopher Bell wrote:
> >
> > Hello Freesurfers,
> >
> >
> > I have developed a pipeline that uses mri_label2vol to take freesurfer
> > parcellations to
> > native fmri space, and uses dilation (within mri_label2vol) to make
> > the ROIs larger since our resolution is only
> > 3.5x3.5x4 we would end up with only a few voxels for some ROIs due to
> > large voxel
> > size and partial voluming wihout the dilation. However, since the lh
> > and rh are done
> > separately by mri_label2vol, I now have overlap on the midline and
> > have to go through a bunch
> > of masking steps to eliminate it.
> >
> > My question is; is there a tool that will take both lh/rh
> > parcellations to a new coordinate
> > system, do dilation, and most importantly control for lh/rh overlap?
> > Or any other
> > similar suggestions. Thanks!
> >
> > Basically I am looking to rework my pipeline, and it seems I should be
> > able
> > to find a more parsimonious solution, than my "Rube Goldberg" approach.
> >
> > Chris
> >
> >
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> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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Re: [Freesurfer] "Splotchy" labels after transformation from fsaverage to native

[Michael Waskom]

Hi, just wanted to bump this up since it looks like Doug is back.

On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom wrote:

> Hi,
>
> I'm using mri_label2label to reverse normalize labels from fsaverage
> space to the native surface.
>
> I'm ending up with some splotchy-looking labels, for lack of a better
> word.  See what I mean here:
> http://web.mit.edu/mwaskom/www/splotchy.png
>
> I'm doing this normalization in a script with the following relevant
> line, which seems to be what happens inthe BAlabes step of recon-all
>
> mri_label2label --srclabel ../fsaverage/label/${hemi}.${roi}.label  \
> --srcsubject fsaverage --trgsubject ${subj} \
> --trglabel label/$hemi.${roi}.label \
> --regmethod surface --hemi $hemi
>
> Any idea how I can avoid this splotchiness or, failing that, do a
> closing on the label to clean up some of the noise?
>
> Cheers,
> Michael
>
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Re: [Freesurfer] parcellations to fmri space

[Douglas N Greve]

So you want to make a particular label bigger (more surface area) on 
cortex?
doug

On 07/16/2012 02:51 PM, Christopher Bell wrote:
>
> I tried using mri_label2vol with --aparc+aseg instead of --aparc. This
> works and provides cortical and subcortical with no overlap. It doesn't
> allow me to do cortical dilation, but that is probably because it 
> wouldn't mesh
> well with the subcortical ROIs. Thanks.
>
> Chris
>
>
> On Mon, Jul 16, 2012 at 9:03 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> Hi Chris, I don't think there is such a tool. One thing you can do
> is to
> use the aparc+aseg.mgz as the source instead of the lh and rh surfaces
> separately. This might solve all of your problems.
> doug
>
>
> On 07/06/2012 12:02 PM, Christopher Bell wrote:
> >
> > Hello Freesurfers,
> >
> >
> > I have developed a pipeline that uses mri_label2vol to take
> freesurfer
> > parcellations to
> > native fmri space, and uses dilation (within mri_label2vol) to make
> > the ROIs larger since our resolution is only
> > 3.5x3.5x4 we would end up with only a few voxels for some ROIs
> due to
> > large voxel
> > size and partial voluming wihout the dilation. However, since the lh
> > and rh are done
> > separately by mri_label2vol, I now have overlap on the midline and
> > have to go through a bunch
> > of masking steps to eliminate it.
> >
> > My question is; is there a tool that will take both lh/rh
> > parcellations to a new coordinate
> > system, do dilation, and most importantly control for lh/rh overlap?
> > Or any other
> > similar suggestions. Thanks!
> >
> > Basically I am looking to rework my pipeline, and it seems I
> should be
> > able
> > to find a more parsimonious solution, than my "Rube Goldberg"
> approach.
> >
> > Chris
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
>
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>
>
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> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
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> but does not contain patient information, please contact the
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> dispose of the e-mail.
>
>

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Phone Number: 617-724-2358
Fax: 617-726-7422

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[Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

[Ayaz, Muhammad]

Dear All,

After running recon-all, I noticed several subjects that sum of WM and GM is 
bigger  than ICV. I have re-run these subjects and the results is the same sum 
of GM and WM is coming out to be bigger than ICV.
Any suggestions? I need to calculate normalized volumes.

Regards
Ayaz


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Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

[Bruce Fischl]

Hi Ayaz

what version are you running? There appears to be an instability in the 
eTIV calculation in just version 5.1 (not before or in the upcoming 5.2)


cheers
Bruce
On 
Mon, 16 Jul 2012, Ayaz, Muhammad wrote:




Dear All,

 

After running recon-all, I noticed several subjects that sum of WM and GM is
bigger  than ICV. I have re-run these subjects and the results is the same
sum of GM and WM is coming out to be bigger than ICV.

Any suggestions? I need to calculate normalized volumes.

 

Regards

Ayaz


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Re: [Freesurfer] "Splotchy" labels after transformation from fsaverage to native

[Douglas N Greve]

There is not an easy/good way to handle this situation. The way it works 
is that it goes through each point in the source and finds the closest 
vertex in the target. If the target is more densely sampled, then there 
are some points in the target in the middle of the label that are not 
the closest vertex to any label vertex in the source. It is hard to 
figure out computationally whether an unlabeled point is in the middle 
of the label or halfway around the brain. One thing that might work ok 
is to save the output as a binary mask (--outmask), then smooth it a 
little (mris_fwhm  or mri_surf2surf), then re-binarize the mask 
(mri_binarize), then convert it to a label  (mri_cor2label --i 
smoothed-and-binarized.mgh --id 1 --surf yoursubject lh white --o 
lh.label.yoursubject).

doug

On 07/16/2012 03:30 PM, Michael Waskom wrote:
> Hi, just wanted to bump this up since it looks like Doug is back.
>
> On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom  > wrote:
>
> Hi,
>
> I'm using mri_label2label to reverse normalize labels from fsaverage
> space to the native surface.
>
> I'm ending up with some splotchy-looking labels, for lack of a better
> word.  See what I mean here:
> http://web.mit.edu/mwaskom/www/splotchy.png
>
> I'm doing this normalization in a script with the following relevant
> line, which seems to be what happens inthe BAlabes step of recon-all
>
> mri_label2label --srclabel ../fsaverage/label/${hemi}.${roi}.label  \
> --srcsubject fsaverage --trgsubject ${subj} \
> --trglabel label/$hemi.${roi}.label \
> --regmethod surface --hemi $hemi
>
> Any idea how I can avoid this splotchiness or, failing that, do a
> closing on the label to clean up some of the noise?
>
> Cheers,
> Michael
>
>
>
>
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

[Ayaz, Muhammad]

Well, I am using version 5.1.0. I have had same issue in fewer subjects when I 
used the older version as well. Any comments about that?

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Monday, July 16, 2012 3:04 PM
To: Ayaz, Muhammad
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV 
after recon-all

Hi Ayaz

what version are you running? There appears to be an instability in the 
eTIV calculation in just version 5.1 (not before or in the upcoming 5.2)

cheers
Bruce
On 
Mon, 16 Jul 2012, Ayaz, Muhammad wrote:

> 
> Dear All,
> 
>  
> 
> After running recon-all, I noticed several subjects that sum of WM and GM is
> bigger  than ICV. I have re-run these subjects and the results is the same
> sum of GM and WM is coming out to be bigger than ICV.
> 
> Any suggestions? I need to calculate normalized volumes.
> 
>  
> 
> Regards
> 
> Ayaz
> 
> 
> The information contained in this message and any attachments is intended
> only for the use of the individual or entity to which it is addressed, and
> may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from
> disclosure under applicable law. If you are not the intended recipient, you
> are prohibited from copying, distributing, or using the information. Please
> contact the sender immediately by return e-mail and delete the original
> message from your system.
>


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Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV after recon-all

[Bruce Fischl]

can you send us an example? In the ones we've looked at the older versions 
were more stable. Alternatively, we can send you a new template that Avi 
Snyder generated that you could try out


cheers
Bruce


On Mon, 16 Jul 2012, 
Ayaz, Muhammad wrote:



Well, I am using version 5.1.0. I have had same issue in fewer subjects when I 
used the older version as well. Any comments about that?

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Monday, July 16, 2012 3:04 PM
To: Ayaz, Muhammad
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] sum of WM and GM coming out to be bigger than ICV 
after recon-all

Hi Ayaz

what version are you running? There appears to be an instability in the
eTIV calculation in just version 5.1 (not before or in the upcoming 5.2)

cheers
Bruce
On
Mon, 16 Jul 2012, Ayaz, Muhammad wrote:



Dear All,

 

After running recon-all, I noticed several subjects that sum of WM and GM is
bigger  than ICV. I have re-run these subjects and the results is the same
sum of GM and WM is coming out to be bigger than ICV.

Any suggestions? I need to calculate normalized volumes.

 

Regards

Ayaz


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only for the use of the individual or entity to which it is addressed, and
may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from
disclosure under applicable law. If you are not the intended recipient, you
are prohibited from copying, distributing, or using the information. Please
contact the sender immediately by return e-mail and delete the original
message from your system.




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[Freesurfer] plotting cortical parcellation surfaces using 2009 atlas

[Maria Kharitonova]

Hello,

I apologize if my question is too basic, but I am trying to pull up cortical 
parcellation surfaces for my data, like shown here: 
http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation

I tried typing in "tksurfer subjec_number lh inflated -aparc", but that 
produces the lateral surface using the 2005 atlas. Can you help me by 
suggesting which command can pull up parcellated surfaces using the 2009 atlas? 
Putting in "-aparc.a2009s" does not seem to work (no parcellation is shown). I 
would like to see both lateral and medial surfaces, if possible.

Thank you in advance!
Sincerely,

Maria 



Maria Kharitonova, Ph.D.
Laboratory of Cognitive Neuroscience
Children's Hospital Boston
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Re: [Freesurfer] plotting cortical parcellation surfaces using 2009 atlas

[Bruce Fischl]

Hi Maria

you can use the file menu to load the parcellation (file->label->import 
annotation or something like that), then use the file browser to select the 
one you want.

cheers
Bruce


On Mon, 16 Jul 2012, Maria 
Kharitonova wrote:

> Hello,
>
> I apologize if my question is too basic, but I am trying to pull up cortical 
> parcellation surfaces for my data, like shown here: 
> http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
>
> I tried typing in "tksurfer subjec_number lh inflated -aparc", but that 
> produces the lateral surface using the 2005 atlas. Can you help me by 
> suggesting which command can pull up parcellated surfaces using the 2009 
> atlas? Putting in "-aparc.a2009s" does not seem to work (no parcellation is 
> shown). I would like to see both lateral and medial surfaces, if possible.
>
> Thank you in advance!
> Sincerely,
>
> Maria
>
>
> 
> Maria Kharitonova, Ph.D.
> Laboratory of Cognitive Neuroscience
> Children's Hospital Boston
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[Freesurfer] Restart from somewhere in the middle of mri_ca_register

[Joshua Lee]

Is it possible/pracitcal? This is a long step, and unfortunately my
analysis computer was rebooted in the middle of this step, and I was hoping
to present the volumes tomorrow.. ouch.
-
Josh
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Re: [Freesurfer] ROI functional & anatomical cross

[Huiting Liu]

Hi Doug,

Thank you, I think that will work. Right now my anatomical ROIs are in
subject native space and I would like to register the third-level
group (across subject) fmri activation map to subject native space as well
before crossing the two. Is that possible? I have the anat2exf.register.dat
files for each subjects's group feat (across runs) but I don't know how to
do it for the third level?

Thanks so much,
Huiting


On Mon, Jul 16, 2012 at 2:03 PM, Douglas N Greve
wrote:

> You can create a binary mask of the ROI, then use mri_mask to mask out
> the non-ROI part from the fMRI. does that work?
> doug
>
> On 07/11/2012 11:25 AM, Huiting Liu wrote:
> >
> > Hello,
> >
> >
> > I'm trying to do an ROI analysis that crosses the group-level
> > functional activation with specific anatomical structures. Currently
> > the clusters found for our group-level functional activation are too
> > large and need to be separated into many structures. Is there a
> > command I could use that would cross the group level map with each
> > cortical structure generated by freesurfer's recon-all?
> >
> >
> > Thanks.
> >
> >
> >
> > ___
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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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>
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Re: [Freesurfer] Restart from somewhere in the middle of mri_ca_register

[Bruce Fischl]

no, sorry :<
On Mon, 16 Jul 2012, Joshua Lee wrote:

> Is it possible/pracitcal? This is a long step, and unfortunately my analysis
> computer was rebooted in the middle of this step, and I was hoping to
> present the volumes tomorrow.. ouch.
> -
> Josh
> 
> 
>
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Re: [Freesurfer] Restart from somewhere in the middle of mri_ca_register

[Joshua Lee]

not that I have any real hope  lol
-
Josh


On Mon, Jul 16, 2012 at 1:41 PM, Joshua Lee  wrote:

> Is it possible/pracitcal? This is a long step, and unfortunately my
> analysis computer was rebooted in the middle of this step, and I was hoping
> to present the volumes tomorrow.. ouch.
> -
> Josh
>
>
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Re: [Freesurfer] Restart from somewhere in the middle of mri_ca_register

[Joshua Lee]

Yeah I didn't think so..well my fault for trying to push 30 brains through
at a time on just 24 cores and 24 Gigs of RAM, and all started within 10
minutes of each other..froze her up and locked others out. Ahh, well.
Thanks Bruce and crew!
-
Josh


On Mon, Jul 16, 2012 at 1:58 PM, Bruce Fischl wrote:

> no, sorry :<
>
> On Mon, 16 Jul 2012, Joshua Lee wrote:
>
>  Is it possible/pracitcal? This is a long step, and unfortunately my
>> analysis
>> computer was rebooted in the middle of this step, and I was hoping to
>> present the volumes tomorrow.. ouch.
>> -
>> Josh
>>
>>
>>
>>
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/**complianceline.
>  If the e-mail was sent to you in error
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> properly
> dispose of the e-mail.
>
>
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[Freesurfer] recon-all for non-human primates failed and what to do next?

[Leon]

Hi, FreeSurfer experts. 

I have successfully used FreeSurfer to reconstruct monkey brains, but when I 
used the same scripts on chimpanzees, it failed miserably (see the attached 
figure). I tried several strategies, such as normalizing the wm.mgz to 110, but 
the scripts still did not work. Could someone tell me what other strategies I 
could use to make it work? 


Many thanks in advance!
Leon
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Re: [Freesurfer] "Splotchy" labels after transformation from fsaverage to native

[Michael Waskom]

Hmm, ok.  Are there no functions for doing a dilation/erosion on a surface
label?

On Mon, Jul 16, 2012 at 1:14 PM, Douglas N Greve
wrote:

> There is not an easy/good way to handle this situation. The way it works
> is that it goes through each point in the source and finds the closest
> vertex in the target. If the target is more densely sampled, then there
> are some points in the target in the middle of the label that are not
> the closest vertex to any label vertex in the source. It is hard to
> figure out computationally whether an unlabeled point is in the middle
> of the label or halfway around the brain. One thing that might work ok
> is to save the output as a binary mask (--outmask), then smooth it a
> little (mris_fwhm  or mri_surf2surf), then re-binarize the mask
> (mri_binarize), then convert it to a label  (mri_cor2label --i
> smoothed-and-binarized.mgh --id 1 --surf yoursubject lh white --o
> lh.label.yoursubject).
>
> doug
>
> On 07/16/2012 03:30 PM, Michael Waskom wrote:
> > Hi, just wanted to bump this up since it looks like Doug is back.
> >
> > On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom  > > wrote:
> >
> > Hi,
> >
> > I'm using mri_label2label to reverse normalize labels from fsaverage
> > space to the native surface.
> >
> > I'm ending up with some splotchy-looking labels, for lack of a better
> > word.  See what I mean here:
> > http://web.mit.edu/mwaskom/www/splotchy.png
> >
> > I'm doing this normalization in a script with the following relevant
> > line, which seems to be what happens inthe BAlabes step of recon-all
> >
> > mri_label2label --srclabel ../fsaverage/label/${hemi}.${roi}.label  \
> > --srcsubject fsaverage --trgsubject ${subj} \
> > --trglabel label/$hemi.${roi}.label \
> > --regmethod surface --hemi $hemi
> >
> > Any idea how I can avoid this splotchiness or, failing that, do a
> > closing on the label to clean up some of the noise?
> >
> > Cheers,
> > Michael
> >
> >
> >
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
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>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> dispose of the e-mail.
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Re: [Freesurfer] "Splotchy" labels after transformation from fsaverage to native

[Bruce Fischl]

Hi Michael,

yes, you can do this in tksurfer with a tcl script (labl_erode and 
labl_dilate I believe). Not sure if there is a binary to do it, but it 
would be pretty easy to write

Bruce


On Mon, 16 Jul 2012, Michael Waskom wrote:


Hmm, ok.  Are there no functions for doing a dilation/erosion on a surface
label?

On Mon, Jul 16, 2012 at 1:14 PM, Douglas N Greve 
wrote:
  There is not an easy/good way to handle this situation. The way
  it works
  is that it goes through each point in the source and finds the
  closest
  vertex in the target. If the target is more densely sampled,
  then there
  are some points in the target in the middle of the label that
  are not
  the closest vertex to any label vertex in the source. It is hard
  to
  figure out computationally whether an unlabeled point is in the
  middle
  of the label or halfway around the brain. One thing that might
  work ok
  is to save the output as a binary mask (--outmask), then smooth
  it a
  little (mris_fwhm  or mri_surf2surf), then re-binarize the mask
  (mri_binarize), then convert it to a label  (mri_cor2label --i
  smoothed-and-binarized.mgh --id 1 --surf yoursubject lh white
  --o
  lh.label.yoursubject).

  doug

  On 07/16/2012 03:30 PM, Michael Waskom wrote:
  > Hi, just wanted to bump this up since it looks like Doug is
  back.
  >
  > On Tue, Jul 10, 2012 at 5:09 PM, Michael Waskom
   > wrote:
>
>     Hi,
>
>     I'm using mri_label2label to reverse normalize labels from
fsaverage
>     space to the native surface.
>
>     I'm ending up with some splotchy-looking labels, for lack of a
better
>     word.  See what I mean here:
>     http://web.mit.edu/mwaskom/www/splotchy.png
>
>     I'm doing this normalization in a script with the following
relevant
>     line, which seems to be what happens inthe BAlabes step of
recon-all
>
>     mri_label2label --srclabel
../fsaverage/label/${hemi}.${roi}.label  \
>                     --srcsubject fsaverage --trgsubject ${subj} \
>                     --trglabel label/$hemi.${roi}.label \
>                     --regmethod surface --hemi $hemi
>
>     Any idea how I can avoid this splotchiness or, failing that, do
a
>     closing on the label to clean up some of the noise?
>
>     Cheers,
>     Michael
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] multiple comparisons correction

[Meng Li]

Dear professor,
 
Thanks for your reply.
 
You said that when drawing conclusions from both hemispheres then I need to use 
.025, but I found that in qdec interface, the default value of -cwpvalue is 
0.05. So are they inconsistent?
 
I also want to find a solution about an ERROR.
I tried to run a cortical thickness analysis to look for differences between 
two groups (patients and controls) with regressing out the gender factor, the 
patients group have 1 female and 17 male, after analysis, I got the results. 
But when I add another continuous variable as covariate,  I received the 
message: "ERROR: matrix is ill-conditioned or badly scaled."  Then I tried to 
change the gender composition the patients groups: 2 female/16 male, and the 
problem was solved. so is it right about what i did, or I need another way to 
solve this problem?

 
Thanks,
 
Best wishes
 
Meng


 
 
 
On 07/06/2012 10:00 PM, Meng Li wrote:
> Hi, freesurfer expert,
> I performed the statistical analysis between two groups first in left 
> hemisphere, and got some regions which showed different.
> 1) so if I then do multiple correction, i don't need to run the 
> mri_glmfit-sim command, and just press the button of the monte carlo 
> null-z simulation in the qdec interface, am i right?
correct
> 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec 
> get the same results, or not?  and as to the option --cwpvalthresh, 
> should i choose 0.05 or 0.025?
If you are drawing conclusions from both hemispheres then you need to 
use .025
> 3) And what is the difference between fdr and mc-z correction?
mc-z uses a cluster-wise correction and controls the rate of false 
positive clusters. FDR is voxel-wise and controls the false discovery 
rate, which is the number of false positives relative to the total 
number of positives (as compared to the number of false positives 
relative to the total number of tests).
 
doug
> Thanks,



--
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