[Freesurfer] Postdoc position at MGH/Harvard

[Jacobs, H (NP)]

External Email - Use Caution

Postdoctoral Opportunity at Mass General Hospital – Harvard Medical School

The Gordon Center for Medical Imaging (GCMI) in the Department of Radiology at 
Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in 
Boston, Massachusetts, has an opening for highly qualified individuals at the 
post-doctoral level to work on research related to multi-modal 7T (f)MRI 
imaging of the brainstem in aging under the mentorship of Dr. Heidi Jacobs. 
This exciting multi-modal project involves dedicated imaging of the brainstem 
nuclei, high-resolution fMRI (possibility to go to layer-fMRI) with 
physiological monitoring, HCP sequences for diffusion imaging and PET-imaging. 
Most of the work in this project will be performed at the Athinoula A. Martinos 
Center for Biomedical Imaging.

The Department of Radiology at MGH is equipped with the first mobile PET/CT, 
the first brain PET/MRI, the first whole-body PET/MRI in the USA and several 
MRI scanners, including two 7T ultra-high-field scanner. It is also equipped 
with a substantial large scale shared memory computing facility for parametric 
image analysis, tomographic reconstruction, Monte Carlo simulation, and other 
computationally intensive research applications.

Applicants must have obtained or anticipate soon receiving a Ph.D. in 
biomedical, computer or electrical engineering, medical physics, cognitive 
neuroscience or a related field. Strong analytical, quantitative and 
programming skills are essential (e.g., QSM, fMRI-physiological data analyses). 
Prior experience in medical imaging, signal/image processing, and physiological 
investigation is advantageous. The successful candidate will have joint 
appointments at MGH and HMS and will be closely interacting with the Harvard 
Aging Brain Study team, the HCP team and the high-field MRI group. If 
interested, please send your CV, letter describing interests, background, 
qualifications and 3 references (including contact details).

MGH & HMS are equal-opportunity, affirmative action employers. Women and 
minority candidates are encouraged to apply.

Heidi Jacobs, Ph.D.

Email: hjac...@mgh.harvard.edu
[cid:image001.png@01D56AA0.20580A50]
Gordon Center for Medical Imaging
MGH – Nashua 6606; Radiology, MGH
125 Nashua Street
Boston, MA 02114





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Re: [Freesurfer] c_ras for HCP compatibility

[Glasser, Matthew]

External Email - Use Caution

Were the images acquired with the animal in a funny position relative to 
humans?  That might be the issue.  I would convert DICOMs to NIFTI prior to 
FreeSurfer, make sure the image is oriented as RPI or LPI and that the labels 
match the brain (e.g. in a tool like FSLView) and then run FreeSurfer.

Matt.

From:  on behalf of Robert Austin Bruce 
Benn 
Reply-To: Freesurfer support list 
Date: Friday, September 13, 2019 at 7:06 AM
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] c_ras for HCP compatibility


External Email - Use Caution
Hi Y’all,

I was wondering if Y’all could tell me how c_ras is calculated in the x_form 
matrix for orig.mgz?

I’ve been using some animal brains, and the pipeline works very well at 
creating surfaces and aligning them to their coresponding image for freeview.
Post pipeline I’ve been applying the cras matix as derived from the orig.mgz to 
remove the offset for use in wb_view.

The commands for applying the transforms work fine.
However I end up getting a surface that is either inverted, or perpendicular to 
the nifti volume in wb_view.

The animal image does have a large field of view, with a relatively small brain.
I think the cras matrix isn’t getting calculated correctly, but that the images 
I’m using may not have a standered cras so I may need to hack around that.

Could you explain to me how c_ras is calculated?
Also if I need to edit c_ras how would I go about doing it? is it derived from 
the q and s forms?

thanks!

austin

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[Freesurfer] Longitudinal stream finalsurfs misalignment?

[Douglas Merkitch]

External Email - Use Caution

Hey all,

I have a group of subjects with 2 time points that I've run thru the 
longitudinal processing stream. All goes OK until I run the recon-all -long and 
the resulting .long. subject dirs have the finalsurfs misaligned (i.e. one 
subject has the edits moved inferior and the other has them moved superior, 
causing drastic consequences to the pial/wm surfaces).

FYI these subjects were processed on a Linux-based high performance computing 
cluster and edits were made locally on a Linux virtual machine with subject 
dirs being transferred back and forth via scp. Not sure if this is relevant, 
but thought I'd mention it just in case.

I've uploaded a .tar file containing one of these longitudinal subject's 
directories (i.e. both cross tps, base, and both resulting long tps) called 
'merkitch_upload_201980913.tar' via the filedrop website.

Any help would be appreciated!

Thanks,

Doug

Douglas Merkitch
Clinical Research Coordinator

355 E. Erie St, Chicago, IL 60611
312-238-5911 office
dmerki...@sralab.org

[cid:image002.jpg@01D56A28.22DB2140]
sralab.org

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[Freesurfer] Questions about labels and tkmedit

[Zeng,Victor (BIDMC - Psychiatry)]

Hi all,

?

I know tkmedit has been deprecated, but we're thinking about using it just for 
quality check purposes since we found that it is less resource intensive. We're 
trying to load multiple labels, is there a way to do that so that each label is 
assigned a different color (we know that's possible for Freeview).


best


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
ph: 617 754 1237
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[Freesurfer] mkcontrast-sess question

[Nasiriavanaki, Zahra]

Dear Freesurfer experts

Hi

I have a question about weighting different contrasts using mkcontrast-sess 
commmand.
I have single subject functional data with 18 different contrasts, and I am 
willing to weight the different contrasts as (for example) ascending linear. 
Something like:
 mkcontrast-sess -an $analysis   -a 1 -a 2 -a 3 -a 4 -a 10 -a 11 -a 12 -a 13 -a 
6 -a 7 -a 8 -a 9 -a 15 -a 16 -a 17 -a 18
 In which contrast number two weights twice as contrast number one and contrast 
number 3 weights twice as contrast number 2 and so on.  Is there any way I can 
do such a thing with mkcontrast-sess? or do you have any suggestion for such an 
analysis?

Thanks
Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

[Greve, Douglas N.,Ph.D.]

This is a bug. I've fixed it in our development version. You can download an 
update from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surf2surf


On 9/13/19 8:00 AM, Matthieu VANHOUTTE wrote:
   External Email - Use Caution
Dear FS's experts,

I am trying to downsample some surface data from fsaverage to fsaverage6 with 
the following command:

 mri_surf2surf --hemi lh --srcsubject fsaverage --sval ./lh.fsaverage.s8mm.mgh  
--trgsubject fsaverage6 --tval ./lh.fsaverage6.s8mm.mgh --cortex

However, the output surface data is a binary file contrary to the source one 
(please see attached).

Would anyone have an idea of the problem?

Best,

Matthieu




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Re: [Freesurfer] timewindow parameter in mkanalysis-sess {Disarmed}

[Caspar M. Schwiedrzik]

External Email - Use Caution

Yes I did. Caspar

On Fri, Sep 13, 2019 at 16:19 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Did you put -timewindow before -gammafit ?
>
>
> On 9/12/19 6:08 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
> Hi Doug,
> apart from the question whether or not to set the timewindow parameter to
> 80 for MION responses, I noticed that there is a discrepancy between
> analysis.info
> 
> and h.dat with regard to this parameter in v5.3.
> If I set timewindow to 80 in mkanalysis-sess, it correctly prints this
> parameter into analysis.info
> .
> However, in h.dat for the same analysis, timewindow is 40.
> I don't know if that is relevant, but it seems weird. Maybe it was already
> addressed in version 6.
>
> Caspar
>
> Am Di., 13. Aug. 2019 um 22:51 Uhr schrieb Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu>:
>
>> That is in response to a 60 sec stimulus. The time window is the time
>> needed to account for a very brief stimulus (ie, the impulse response).
>> fsfast will automatically take into account the duration of the stimulus
>> as listed in the paradigm file.
>>
>> On 8/13/19 2:14 PM, Caspar M. Schwiedrzik wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hi Doug,
>> > Thanks for the advice.
>> > I think the Leite et al. 2002 NeuroImage paper can be interpreted that
>> > way. See Figure 1 and 2.
>> >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__pop.cerco.ups-2Dtlse.fr_pdf0609_leite-5Ffp-5F02-5F283.pdf=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs=_NKVTMtmRmOeLrYx6styS12TMjsFNuVd2jKFxUKr85Y=
>> >
>> > Caspar
>> >
>> > On Tue, Aug 13, 2019 at 17:12 Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > When you use -gammafit, it automatically sets the time window to
>> > 40. If
>> > you really want it at 80, but -timewindow before -gammafit. Do you
>> > really expect the MION hrf to last 80 sec?
>> >
>> > On 8/13/19 11:06 AM, Caspar M. Schwiedrzik wrote:
>> > >
>> > > External Email - Use Caution
>> > >
>> > > Hi!
>> > > I am having difficulties setting the timewindow parameter in
>> > > mkanalysis-sess in Freesurfer v5.3.
>> > > I am trying to use 80 (data acquired with MION), but the parameter
>> > > does not seem to affect analysis.info
>> 
>> <
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs=r6h1NqLGmsc3cSyXVgnrkGSvJNA79vDmmSjMUdNwGOA=
>> >
>> > <
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=CYJUPBXH2fLSD5LjpZmYtjXWz_bC8zt7q5gobDE5VLs=Ba7XLDz4JrZXYf4-uKSwAzN0dCldTpp68Yck9EDkQ4s=
>> > >, where it
>> > > is always 40.
>> > > Is it possible to force a different timewindow?
>> > > Below is some info from analysis.info
>> 
>> <
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs=r6h1NqLGmsc3cSyXVgnrkGSvJNA79vDmmSjMUdNwGOA=
>> >
>> > <
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__analysis.info=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=CYJUPBXH2fLSD5LjpZmYtjXWz_bC8zt7q5gobDE5VLs=Ba7XLDz4JrZXYf4-uKSwAzN0dCldTpp68Yck9EDkQ4s=
>> > >.
>> > > Thanks, Caspar
>> > >
>> > >
>> > > # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> > > # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07
>> > greve
>> > > Exp $
>> > > # MKACMD /neuro_tools/freesurfer/fsfast/bin/mkanalysis-sess 

Re: [Freesurfer] timewindow parameter in mkanalysis-sess

[Greve, Douglas N.,Ph.D.]

Did you put -timewindow before -gammafit ?

On 9/12/19 6:08 AM, Caspar M. Schwiedrzik wrote:

External Email - Use Caution

Hi Doug,
apart from the question whether or not to set the timewindow parameter to 80 
for MION responses, I noticed that there is a discrepancy between 
analysis.info and h.dat with regard to this parameter in 
v5.3.
If I set timewindow to 80 in mkanalysis-sess, it correctly prints this 
parameter into analysis.info. However, in h.dat for the 
same analysis, timewindow is 40.
I don't know if that is relevant, but it seems weird. Maybe it was already 
addressed in version 6.

Caspar

Am Di., 13. Aug. 2019 um 22:51 Uhr schrieb Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>>:
That is in response to a 60 sec stimulus. The time window is the time
needed to account for a very brief stimulus (ie, the impulse response).
fsfast will automatically take into account the duration of the stimulus
as listed in the paradigm file.

On 8/13/19 2:14 PM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
>
> Hi Doug,
> Thanks for the advice.
> I think the Leite et al. 2002 NeuroImage paper can be interpreted that
> way. See Figure 1 and 2.
> https://urldefense.proofpoint.com/v2/url?u=http-3A__pop.cerco.ups-2Dtlse.fr_pdf0609_leite-5Ffp-5F02-5F283.pdf=DwIGaQ=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg=sgvCAzCi3iTXkTNRRVMpDnC6tu0lnijYpKXIX_UNme8=eAOAyZnFl2mF0kq1dbzrVLi05dYWhd00N8Sz06JBRgs=_NKVTMtmRmOeLrYx6styS12TMjsFNuVd2jKFxUKr85Y=
>
> Caspar
>
> On Tue, Aug 13, 2019 at 17:12 Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu> 
> >> wrote:
>
> When you use -gammafit, it automatically sets the time window to
> 40. If
> you really want it at 80, but -timewindow before -gammafit. Do you
> really expect the MION hrf to last 80 sec?
>
> On 8/13/19 11:06 AM, Caspar M. Schwiedrzik wrote:
> >
> > External Email - Use Caution
> >
> > Hi!
> > I am having difficulties setting the timewindow parameter in
> > mkanalysis-sess in Freesurfer v5.3.
> > I am trying to use 80 (data acquired with MION), but the parameter
> > does not seem to affect analysis.info 
>   >
> 
>  >, where it
> > is always 40.
> > Is it possible to force a different timewindow?
> > Below is some info from analysis.info 
>   >
> 
>  >.
> > Thanks, Caspar
> >
> >
> > # FSBUILD freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> > # MKAVERSION $Id: mkanalysis-sess,v 1.64.2.5 2013/01/22 21:52:07
> greve
> > Exp $
> > # MKACMD /neuro_tools/freesurfer/fsfast/bin/mkanalysis-sess -fsd
> bold
> > -native -timeoffset -2/2 -event-related -paradigm .para
> > -nconditions 4 -TR 2 -gammafit 0 8 -gammaexp 0.3 *-timewindow 80*
> > -refeventdur 0.5 -polyfit 2 -hpf 0.0109 -analysis  -funcstem
> 
> > -runlistfile .list -nuisreg motion.dat 6 -tpef tpef.dat
> -acfbins
> > 14 -acffwhm 0 -mask  -force
> >
> >
> > analysis 
> > mcstem fmc
> > funcstem 
> > fsd bold
> > runlistfile .list
> > TR 2
> > RegDOF 6
> > PerSession 1
> > RawSpace volume native
> > mask 
> > RawFWHM 0
> > RawSTC none
> > UseB0DC 0
> > ApplySubCortMask 1
> > inorm 100
> > acfbins 14
> > fixacf  1
> > acffwhm 0
> > acfsvd  0
> > designtype event-related
> > tpexclude tpef.dat
> > nskip 0
> > polyfit 2
> > HPFCutoffHz 0.0109
> > HeteroGCor 0
> > nconditions 4
> > parname .para
> > RefEventDur 0.5
> > *timewindow 40.00*
> > prestim 0
> > TER 0.05
> > gamma 0 8 0.3 0
> > stimulusdelay -2/2
> > Condition 1 Condition01
> > Condition 2 Condition02
> > Condition 3 Condition03
> > 

Re: [Freesurfer] multiple comparisons correction for brain-behaviour correlations

[Greve, Douglas N.,Ph.D.]

I think you could get the p-valueus for the clusters and do FDR on those (or 
maybe the most significant of more than one cluster in a given comparison)

On 9/11/19 9:26 AM, Annelies Vant Westeinde wrote:

External Email - Use Caution

Dear members,

I have run several analyses in which we correlate cognitive performance with 
vertex-wise cortical surface area, thickness and volume. We ran monte carlo 
simulation for each correlation. However, we would like to correct the outcome 
for the number of associations we did, that is for the for 10 different 
cognitive scales that we tested. How can this be done? We would rather not use 
bonferroni correction, as it is so strict, but would prefer fdr. Do we need to 
somehow get the p-values of the cluster peaks that correlated with the 
cognitive scales and do FDR on those? Or should we adjust the monte carlo 
simulation threshold to account for the 10 different tests?

Thank you in advance,

Annelies

Annelies van't Westeinde | PHD Candidate
Department of Women's and Children's Health | Karolinska Institutet
171 77 Solna | Karolinskavägen 37A
+46 760967499
annelies.vant.westei...@ki.se | 
ki.se
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Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

[Bruce Fischl]

oh I see. I thought you meant the file format was not binary. Hmmm, not 
sure. Maybe Doug will have some insight, as I didn't think surf2surf would 
binarize by default

Bruce
On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote:



External Email - Use Caution

Hi Bruce,

The input file has not only binary values (0 or 1) it is made of float
values, whereas the output mri_surf2surf contains only binary values.

Best,

Matthieu

On 13/09/2019 15:52, Bruce Fischl wrote:
  Hi Matthieu

  sorry, I don't understand. All the files are binary, no? Are you
  getting an error?

  cheers
  Bruce
  On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote:

  External Email - Use Caution Dear FS's
experts,

I am trying to downsample some surface data from
fsaverage to fsaverage6 with the following command:

 mri_surf2surf --hemi lh --srcsubject fsaverage
--sval ./lh.fsaverage.s8mm.mgh  --trgsubject
fsaverage6 --tval ./lh.fsaverage6.s8mm.mgh --cortex

However, the output surface data is a binary file
contrary to the source one (please see attached).

Would anyone have an idea of the problem?

Best,

Matthieu




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Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

[Matthieu VANHOUTTE]

   External Email - Use Caution


Hi Bruce,

The input file has not only binary values (0 or 1) it is made of float 
values, whereas the output mri_surf2surf contains only binary values.


Best,

Matthieu

On 13/09/2019 15:52, Bruce Fischl wrote:

Hi Matthieu

sorry, I don't understand. All the files are binary, no? Are you 
getting an error?


cheers
Bruce
On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote:


  External Email - Use Caution Dear FS's experts,

I am trying to downsample some surface data from fsaverage to 
fsaverage6 with the following command:


 mri_surf2surf --hemi lh --srcsubject fsaverage --sval 
./lh.fsaverage.s8mm.mgh  --trgsubject fsaverage6 --tval 
./lh.fsaverage6.s8mm.mgh --cortex


However, the output surface data is a binary file contrary to the 
source one (please see attached).


Would anyone have an idea of the problem?

Best,

Matthieu





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Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

[Bruce Fischl]

Hi Matthieu

sorry, I don't understand. All the files are binary, no? Are you getting 
an error?


cheers
Bruce
On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote:

  External Email - Use Caution 
Dear FS's experts,


I am trying to downsample some surface data from fsaverage to fsaverage6 with 
the following command:


 mri_surf2surf --hemi lh --srcsubject fsaverage --sval 
./lh.fsaverage.s8mm.mgh  --trgsubject fsaverage6 --tval 
./lh.fsaverage6.s8mm.mgh --cortex


However, the output surface data is a binary file contrary to the source one 
(please see attached).


Would anyone have an idea of the problem?

Best,

Matthieu


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Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)

[Bruce Fischl]

glad it worked out
Bruce
On Fri, 13 Sep 2019, 3 6 wrote:



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Hi Bruce,
I checked the alias, I really aliased mv to “mv -i”, and it worked
automatically, after I unaliased.

Thanks for your help.

Best regards,
Guodong

  在
  2019年9月13日，上午12:00，freesurfer-requ...@nmr.mgh.harvard.edu
  写道：

Re: Hippocampal-subfields-T1 interruption (Bruce Fischl)



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[Freesurfer] c_ras for HCP compatibility

[Robert Austin Bruce Benn]

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Hi Y’all,

I was wondering if Y’all could tell me how c_ras is calculated in the x_form 
matrix for orig.mgz?

I’ve been using some animal brains, and the pipeline works very well at 
creating surfaces and aligning them to their coresponding image for freeview.
Post pipeline I’ve been applying the cras matix as derived from the orig.mgz to 
remove the offset for use in wb_view.

The commands for applying the transforms work fine.
However I end up getting a surface that is either inverted, or perpendicular to 
the nifti volume in wb_view.

The animal image does have a large field of view, with a relatively small brain.
I think the cras matrix isn’t getting calculated correctly, but that the images 
I’m using may not have a standered cras so I may need to hack around that.

Could you explain to me how c_ras is calculated?
Also if I need to edit c_ras how would I go about doing it? is it derived from 
the q and s forms?

thanks!

austin


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Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)

[3 6]

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Hi Bruce,

I checked the alias, I really aliased mv to “mv -i”, and it worked 
automatically, after I unaliased.

Thanks for your help.

Best regards,
Guodong

> 在 2019年9月13日，上午12:00，freesurfer-requ...@nmr.mgh.harvard.edu 写道：
> 
> Re: Hippocampal-subfields-T1 interruption (Bruce Fischl)

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