[Freesurfer] Makefile for Tracula

[Kirstie Whitaker]

External Email - Use Caution

Hi everyone!

Firstly - and most importantly - thank you for the awesome tool, and for
all your help in using it!

I'm re-processing (and re-quality controll-ing) data that was formatted in
v5.3 into v6 and I've come to re-running trac-all.

I've been using v6 with the updated Makefile (if anyone's googling this
question, see the note at this page about the fact that v6 doesn't ship
with the correct make file
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0#Tipsandgeneralquestions
).

I wonder if a) there is a makefile for trac-all (that would be amazing) or
b) you could tell me which files I need to delete so I re-process them now
that the surfaces are updated? I assume the DTI processing hasn't changed,
so I shouldn't need to change the bedpostx folder for example, but I'm not
100% sure on which other files have dependences on the reconstructions :)

(The surfaces got pretty messed up in this update so I'd like to go back to
basicswithout having to rerun things we KNOW aren't related to the
surface reconstructions.)

Thank you!
Kirstie

-- 
Kirstie Whitaker, PhD

Research Fellow, Alan Turing Institute
Research Associate, University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* https://whitakerlab.github.io
*Twitter:* @kirstie_j <https://twitter.com/kirstie_j>
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Re: [Freesurfer] Version 6.0.0 or 6.0.1?

[Kirstie Whitaker]

External Email - Use Caution

Thank you for clarifying.

One big problem was the error in the make file and I think I'm still
somewhat suffering from that even though I've replaced the file. The short
answer is that if I run recon-all -make all on the same subject twice it
will re-run recon-all on that second occasion...I don't know why make isn't
detecting that I had just run the command! (There must be an error - it's
just strange that it happens on approx 5% of all my scans but in no
discernable way!)

The main thing I'm trying to do is move from 5.3 to 6.0 processing while
keeping the quality control edits that we've spent a lot of time on. We
have quantitative R1 maps which means recon-all isn't tuned for the maps
and we've done a lot of rounds of manual edits that I don't want to lose!

So if anyone knows exactly which files should be copied across to a new
folder from our 5.3 backup that will allow 6.0 to run recon-all but still
put the surfaces in around about the same place that would be great :)

I don't think this will be fixed with 6.0.1! Thank you for clarifying :)

Kx

On Tue, 11 Dec 2018 at 18:36, Hoopes, Andrew 
wrote:

> Hi Kirstie, sorry for the lack of documentation – there’s practically no
> difference between 6.0.0 and 6.0.1. The only update in 6.0.1 is the ability
> to point to an external license using the FS_LICENSE environment variable.
> What kind of issues are you having with 6.0.0?
>
>
>
> Best,
>
> Andrew
>
>
>
>
>
> *From: * on behalf of Kirstie
> Whitaker 
> *Reply-To: *FS Help 
> *Date: *Tuesday, December 11, 2018 at 4:28 AM
> *To: *FS Help 
> *Subject: *[Freesurfer] Version 6.0.0 or 6.0.1?
>
>
>
> *External Email - Use Caution*
>
> Hi Freesurfer team,
>
>
>
> On the download website version 6.0.0 is linked:
> https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
>
>
>
> But on this list there has been discussion of version 6.0.1 which can be
> downloaded from
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1
>
>
>
> What's the recommended version to use?
>
>
>
> I've been using 6.0.0 but with an updated make file following the
> instructions in this email:
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-April/056644.html
> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-April/056644.html>
>
>
>
> Is the makefile updated in 6.0.1? Are there any other differences? I'm
> having a lot of difficulty getting recon-all to run reliably with 6.0.0
> (some subjects are fine, others not!) and I'm wondering if that's because
> I'm supposed to be using 6.0.1?
>
>
>
> Thank you for your help!
>
> Kirstie
>
>
>
> --
>
> Kirstie Whitaker, PhD
>
>
>
> Research Fellow, Alan Turing Institute
>
> Research Associate, University of Cambridge
>
>
> *Mailing Address*
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
>
> *Phone: *+44 7583 535 307
>
> *Website:* https://whitakerlab.github.io
>
> *Twitter:* @kirstie_j <https://twitter.com/kirstie_j>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
Kirstie Whitaker, PhD

Research Fellow, Alan Turing Institute
Research Associate, University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* https://whitakerlab.github.io
*Twitter:* @kirstie_j <https://twitter.com/kirstie_j>
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[Freesurfer] Version 6.0.0 or 6.0.1?

[Kirstie Whitaker]

External Email - Use Caution

Hi Freesurfer team,

On the download website version 6.0.0 is linked:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

But on this list there has been discussion of version 6.0.1 which can be
downloaded from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1

What's the recommended version to use?

I've been using 6.0.0 but with an updated make file following the
instructions in this email:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-April/056644.html

Is the makefile updated in 6.0.1? Are there any other differences? I'm
having a lot of difficulty getting recon-all to run reliably with 6.0.0
(some subjects are fine, others not!) and I'm wondering if that's because
I'm supposed to be using 6.0.1?

Thank you for your help!
Kirstie

-- 
Kirstie Whitaker, PhD

Research Fellow, Alan Turing Institute
Research Associate, University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* https://whitakerlab.github.io
*Twitter:* @kirstie_j <https://twitter.com/kirstie_j>
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Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

[Kirstie Whitaker]

Hi Foucalt,

I think you need to set the threshold to slightly larger than 0 otherwise
you're taking the center of mass of the whole image (including the 0s) when
really you want to exclude the 0s and only look at the individual regions.

I changed --thmin 0  to --thmin 0.1 and the results looked good.

Kx

On 21 February 2018 at 09:28, zuxfoucault Wong <zuxfouca...@gmail.com>
wrote:

> Attach name file and result file.
>
> Thank you for your time!
>
> Best,
> Foucault
>
> On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong <zuxfouca...@gmail.com>
> wrote:
>
>> Hi Kirstie,
>>
>> Thank you very much for the suggestions!
>> I modified my snippet to prevent it from looping the same value and still
>> got the same results?
>>
>> ##
>> input=($(cat ./names_68parc.txt))
>> labels=()
>> hemis=()
>> j=0
>> for i in "${input[@]}"; do
>> if [[ $i == lh_* ]]; then
>> hemis[j]="lh"
>> i=$(echo $i | sed 's/^lh_//g')
>> labels[j]="$i"
>> (( j++ ))
>> elif [[ $i == rh_* ]]; then
>> hemis[j]="rh"
>> i=$(echo $i | sed 's/^rh_//g')
>> labels[j]="$i"
>> (( j++ ))
>> fi
>> done
>>
>> nlabel=68
>> if [[ ${#labels[@]} != $nlabel ]] && [[ ${#hemi[@]} != $nlabel ]]; then
>> echo " number of label not match "
>> fi
>>
>>
>> for hemi in lh rh; do
>> mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir ./labels
>> done
>>
>> for ((i=0;i<${#labels[@]};i++)); do
>> mri_surfcluster --in /usr/local/freesurfer_orig/sub
>> jects/fsaverage/surf/${hemis[i]}.thickness --clabel
>> ./labels/${hemis[i]}.${labels[i]}.label --sum
>> ./labels/sum.${hemis[i]}.${labels[i]} --centroid --thmin 0 --hemi
>> ${hemis[i]} --subject fsaverage
>> tail -1 ./labels/sum.${hemis[i]}.${labels[i]} | sed 's/  */ /g' | cut
>> -d' ' -f6-8 >> ./labels/68parc.centroids.txt
>> done
>> ##
>>
>>
>> The output message of mri_surfcluster:
>> ##
>> thsign = abs, id = 0
>> version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman
>> Exp $
>> hemi   = rh
>> srcid  = /usr/local/freesurfer_orig/sub
>> jects/fsaverage/surf/rh.thickness
>> srcsubjid  = fsaverage
>> srcsurf= white
>> srcframe   = 0
>> thsign = abs
>> thmin  = 0
>> thmax  = -1
>> fdr= -1
>> minarea= 0
>> xfmfile= talairach.xfm
>> clabelfile = ./labels/rh.lateraloccipital.label
>> clabelinv  = 0
>> nth = -1
>> sumfile  = ./labels/sum.rh.lateraloccipital
>> subjectsdir= /usr/local/freesurfer_orig/subjects
>> FixMNI = 1
>> Loading clabel ./labels/rh.lateraloccipital.label.
>> Found 5963 points in clabel.
>> - XFM matrix (RAS2RAS) ---
>> /usr/local/freesurfer_orig/subjects/fsaverage/mri/transforms
>> /talairach.xfm
>>  1.0   0.0   0.0   0.0;
>>  0.0   1.0   0.0   0.0;
>>  0.0   0.0   1.0   0.0;
>>  0.0   0.0   0.0   1.0;
>> 
>> Reading source surface /usr/local/freesurfer_orig/sub
>> jects/fsaverage/surf/rh.white
>> Done reading source surface
>> Computing metric properties
>> Loading source values
>> number of voxels in search space = 5963
>> Done loading source values (nvtxs = 163842)
>> overall max = 3.19752 at vertex 122846
>> overall min = 0 at vertex 0
>> surface nvertices 163842
>> metric props tot surface area 65020.839844
>> group_avg_vtxarea_loaded 1
>> masked surface area 4459.747559
>> NOT Adjusting threshold for 1-tailed test
>> thminadj = 0
>> Searching for Clusters ...
>> thmin=0.00 (0.00), thmax=-1.00 (-1), thsignid=0,
>> minarea=0.00
>> Found 1 clusters
>> Max cluster size 82167.00
>> INFO: fixing MNI talairach coordinates
>>
>>
>> On Wed, Feb 21, 2018 at 3:15 PM, Kirstie Whitaker <kw...@cam.ac.uk>
>> wrote:
>>
>>> Hi Foucault,
>>>
>>> In the snippet you added you don’t define the labels variable (which you
>>> subsequently loop over in for label in ${labels}).
>>>
>>> There are two possible mistakes that are easy to fix. One may be that
>>> you forgot to read in the labels! And the other is that to get all the
>>> values in an array you need ${labels[@]}.
>>>
>>> I

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

[Kirstie Whitaker]

Hi Foucault,

In the snippet you added you don’t define the labels variable (which you 
subsequently loop over in for label in ${labels}).

There are two possible mistakes that are easy to fix. One may be that you 
forgot to read in the labels! And the other is that to get all the values in an 
array you need ${labels[@]}.

I don’t think you need greater precision than you have. The regions are pretty 
far apart in mm terms :)

Kirstie

Sent from my iPhone, please excuse any typos or excessive brevity

> On 21 Feb 2018, at 03:44, zuxfoucault Wong  wrote:
> 
> Dear Freesurfer experts,
> 
> Based on this 
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/07.html
>  , I wrote a short script to extract the centroids from Desikan-Killiany 
> atlas. 
> 
> ##
> for hemi in lh rh; do
>   mri_annotation2label --subject fsaverage --hemi ${hemi} --outdir 
> ./labels
>   for label in ${labels}; do
>   mri_surfcluster --in 
> /usr/local/freesurfer/subjects/fsaverage/surf/${hemi}.thickness --clabel 
> ./labels/${label}.label --sum ./labels/sum.${label} --centroid --thmin 0 
> --hemi ${hemi} --subject fsaverage
>   tail -1 ./labels/sum.${label} | sed 's/  */ /g' | cut -d' ' 
> -f6-8 >> ./labels/68parc.centroids.txt
>   done
> done
> ###
> 
> However, 1) the value is not precise enough, it is only one digit after 
> decimal point. And 2) I kept getting the same value for each hemisphere.
> Eg,.
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0
> 29.8 -20.7 18.0  
> 
> I would appreciate if you have any suggestions regarding extracting centroids 
> and the aforementioned issues!
> Thank you for your time!
> 
> Best,
> Foucault
> 
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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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Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing

[Kirstie Whitaker]

Hi freesurfer team,

I just ran into this error. I fixed it by switching from python 3.6 to
python 2.7.

Does this sound like the right fix? I wonder if it is documented somewhere
on the wiki?

Thank you for the great tool!
Kx

On 18 November 2016 at 21:14, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> what happens when you run  asegstats2table --help
>
> It does not fail for me. I wonder if it is a python version problem
>
>
> On 11/18/2016 04:01 PM, Elijah Mak wrote:
> > Hi ZK,
> >
> > Thanks. It is great news! I would like to report the following.
> >
> > asegstats2table seems to be acting strangely.
> >
> >  File "/Applications/freesurfer_b6/bin/asegstats2table", line 195
> >
> > print 'ERROR: subjects are not specified (use --subjects SUBJECTS)'
> >
> > Even typing asegstats2table --help leads to the same error message.
> > It was not found in a prev dev built or in 5.3.
> >
> > Thanks.
> >
> > Also, not sure if it's placebo, but  freeview seems to be running
> > quicker now.
> >
> > Best Wishes,
> >
> > Elijah
> >
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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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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> properly
> dispose of the e-mail.
>
>


-- 
Kirstie Whitaker, PhD
Mozilla Fellow for Science
<https://science.mozilla.org/programs/fellowships>

Postdoctoral researcher
Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
*Twitter:* @kirstie_j <https://twitter.com/kirstie_j>
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Re: [Freesurfer] Quality control with different pipelines

[Kirstie Whitaker]

Brilliant - many thanks.

Kx

On 22 June 2016 at 14:57, Harms, Michael <mha...@wustl.edu> wrote:

>
> Yes on all fronts.
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kirstie
> Whitaker <kw...@cam.ac.uk>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Wednesday, June 22, 2016 at 8:55 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Quality control with different pipelines
>
> Thank you Michael!
>
> So - just to be super sure I'm on the same page here. If I've run a
> subject using 5.3 I take that same subject directory (after backing it up
> somewhere) and then run the dev version of recon-all with the -all flag.
> After it's completed I (should - contingent on checking again as you
> recommend) have a well edited subject who can now be reported as having
> been processed with the dev version, right?
>
> Thanks again
> Kx
>
> On 22 June 2016 at 14:48, Harms, Michael <mha...@wustl.edu> wrote:
>
>>
>> Hi,
>> You can simply rerun 'recon-all -all’ on top of your already
>> processed/edited subject, and it will respect your previous edits.  Of
>> course, it is a good idea to still review/QC the results afterwards, to
>> make sure that the outcome of those edits is satisfactory under the new FS
>> version.
>>
>> And, if you want to preserve your results under FS 5.3, then you should
>> make a copy of those results before rerunning recon-all.
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kirstie
>> Whitaker <kw...@cam.ac.uk>
>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Date: Wednesday, June 22, 2016 at 1:28 AM
>> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>> Subject: [Freesurfer] Quality control with different pipelines
>>
>> Hi everyone,
>>
>> I processed and edited 300 participants for our study using Freesurfer
>> 5.3 and I'd like to move to using the dev version that's currently
>> available because we have a bunch more data that's been collected and I
>> think it does a better job. (This question also applies to moving to v 6
>> when it is released).
>>
>> If I run the dev version of recon-all and then copy over the control
>> points and wm.mgz files that we edited in the original run, and run
>> recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very
>> good approximation for the edits we conducted? Or does this "shortcut" not
>> do what I think it does?
>>
>> Does anyone have any experience moving from one version of freesurfer to
>> another without having to start from square one with the edits?
>>
>> Thank you again for the fantastic tools!
>>
>> Kx
>>
>>
>> --
>> Kirstie Whitaker, PhD
>> Research Associate
>>
>> Department of Psychiatry
>> University of Cambridge
>>
>> *Mailing Address*
>> Brain Mapping Unit
>> Department of Psychiatry
>> Sir William Hardy Building
>> Downing Street
>> Cambridge CB2 3EB
>>
>> *Phone: *+44 7583 535 307
>> *Website:* www.kirstiewhitaker.com
>>
>>
>> --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/

Re: [Freesurfer] Quality control with different pipelines

[Kirstie Whitaker]

Thank you Michael!

So - just to be super sure I'm on the same page here. If I've run a subject
using 5.3 I take that same subject directory (after backing it up
somewhere) and then run the dev version of recon-all with the -all flag.
After it's completed I (should - contingent on checking again as you
recommend) have a well edited subject who can now be reported as having
been processed with the dev version, right?

Thanks again
Kx

On 22 June 2016 at 14:48, Harms, Michael <mha...@wustl.edu> wrote:

>
> Hi,
> You can simply rerun 'recon-all -all’ on top of your already
> processed/edited subject, and it will respect your previous edits.  Of
> course, it is a good idea to still review/QC the results afterwards, to
> make sure that the outcome of those edits is satisfactory under the new FS
> version.
>
> And, if you want to preserve your results under FS 5.3, then you should
> make a copy of those results before rerunning recon-all.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kirstie
> Whitaker <kw...@cam.ac.uk>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Wednesday, June 22, 2016 at 1:28 AM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] Quality control with different pipelines
>
> Hi everyone,
>
> I processed and edited 300 participants for our study using Freesurfer 5.3
> and I'd like to move to using the dev version that's currently available
> because we have a bunch more data that's been collected and I think it does
> a better job. (This question also applies to moving to v 6 when it is
> released).
>
> If I run the dev version of recon-all and then copy over the control
> points and wm.mgz files that we edited in the original run, and run
> recon-all with the "-autorecon2-cp -autorecon3" flags will that be a very
> good approximation for the edits we conducted? Or does this "shortcut" not
> do what I think it does?
>
> Does anyone have any experience moving from one version of freesurfer to
> another without having to start from square one with the edits?
>
> Thank you again for the fantastic tools!
>
> Kx
>
>
> --
> Kirstie Whitaker, PhD
> Research Associate
>
> Department of Psychiatry
> University of Cambridge
>
> *Mailing Address*
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
>
> *Phone: *+44 7583 535 307
> *Website:* www.kirstiewhitaker.com
>
>
> --
>
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-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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[Freesurfer] Quality control with different pipelines

[Kirstie Whitaker]

Hi everyone,

I processed and edited 300 participants for our study using Freesurfer 5.3
and I'd like to move to using the dev version that's currently available
because we have a bunch more data that's been collected and I think it does
a better job. (This question also applies to moving to v 6 when it is
released).

If I run the dev version of recon-all and then copy over the control points
and wm.mgz files that we edited in the original run, and run recon-all with
the "-autorecon2-cp -autorecon3" flags will that be a very good
approximation for the edits we conducted? Or does this "shortcut" not do
what I think it does?

Does anyone have any experience moving from one version of freesurfer to
another without having to start from square one with the edits?

Thank you again for the fantastic tools!

Kx


-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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[Freesurfer] Accuracy of D-K atlas for different age ranges

[Kirstie Whitaker]

Hi Freesurfer community,

A reviewer has asked how accurate the application of freesurfer regional
labels are to different age ranges (specifically our study is between 14
and 24 years old).

I'm sure this question has been answered elsewhere so please do forgive me
for being lazy and simply asking you to recommend good references rather
than searching for them in PubMed!

Thank you!

Kirstie x

-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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Re: [Freesurfer] Visualising regional values on the surface

[Kirstie Whitaker]

Brilliant - I think that's probably my friend!

Thanks again everyone for all the help!
Kx

On 29 March 2016 at 16:50, Michael Waskom <mwas...@stanford.edu> wrote:

> Hi Kirstie,
>
> Nibabel has a write_annot function that should work:
> http://nipy.bic.berkeley.edu/nightly/nibabel/doc/reference/nibabel.freesurfer.html#write-annot
>
> Best,
> Michael
>
> On Tue, Mar 29, 2016 at 8:48 AM, Kirstie Whitaker <kw...@cam.ac.uk> wrote:
>
>> Thank you Michael! I <3 Pysurfer.
>>
>> (and freesurfer of course!)
>>
>> The *real* goal is to integrate the code that I've written as a wrapper
>> around pysurfer to show regional values (exactly as you suggest) with
>> BrainNet <https://www.nitrc.org/projects/bnv/> which can show the
>> network nicely on top of freesurfer files.
>>
>> Here's the wiki for my pysurfer wrapper:
>> https://github.com/KirstieJane/DESCRIBING_DATA/wiki/Making-Surface-Plots-with-Pysurfer
>>
>> And the code itself
>> https://github.com/KirstieJane/DESCRIBING_DATA/blob/master/VISUALIZING_SURFACE_MRI_DATA/pysurfer_plot_500parcellation_surface_values.py
>>
>> Unfortunately I don't use BrainNet so I'm having difficulty helping my
>> lab mate make his pretty plots of network nodes and edges overlayed on top
>> of surface colors (eg: modular partition)!
>>
>> Is there a way of writing out an annot file from pysurfer into freesurfer
>> format? Maybe that would bring the two packages closer together
>>
>> Kx
>>
>>
>>
>>
>>
>> On 29 March 2016 at 16:29, Michael Waskom <mwas...@stanford.edu> wrote:
>>
>>> Hi Kirstie,
>>>
>>> Here's an example of how to do this in PySurfer:
>>> http://pysurfer.github.io/examples/plot_parc_values.html
>>>
>>> Hope that helps,
>>> Michael
>>>
>>> On Tue, Mar 29, 2016 at 8:08 AM, dgw <dgwake...@gmail.com> wrote:
>>>
>>>> Hi Kirstie,
>>>>
>>>> You could write your own CLUT file with the color corresponding to the
>>>> correlation you want to show?
>>>> Just open up the file and play with the values in the color columns.
>>>> Then simply load the color table in Freeview and use it to visualize
>>>> the annotation.
>>>>
>>>> There are of course other ways, but this is probably the quickest.
>>>>
>>>> hth
>>>> d
>>>>
>>>>
>>>> On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker <kw...@cam.ac.uk>
>>>> wrote:
>>>> > Hi,
>>>> >
>>>> > I'd like to show correlation coefficients by region on the brain
>>>> surface. So
>>>> > for example, if I've calculated a modular decomposition in a network
>>>> > analysis for each region of the D-K atlas I'd like to be able to
>>>> color each
>>>> > atlas region according to the module it has been assigned to.
>>>> >
>>>> > It seems like I have to do something with the ?h.aparc.annot files
>>>> and a
>>>> > colour lookup table but I'm not sure exactly what.
>>>> >
>>>> > Thank you!
>>>> > Kx
>>>> >
>>>> > --
>>>> > Kirstie Whitaker, PhD
>>>> > Research Associate
>>>> >
>>>> > Department of Psychiatry
>>>> > University of Cambridge
>>>> >
>>>> > Mailing Address
>>>> > Brain Mapping Unit
>>>> > Department of Psychiatry
>>>> > Sir William Hardy Building
>>>> > Downing Street
>>>> > Cambridge CB2 3EB
>>>> >
>>>> > Phone: +44 7583 535 307
>>>> > Website: www.kirstiewhitaker.com
>>>> >
>>>> > ___
>>>> > Freesurfer mailing list
>>>> > Freesurfer@nmr.mgh.harvard.edu
>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> >
>>>> >
>>>> > The information in this e-mail is intended only for the person to
>>>> whom it is
>>>> > addressed. If you believe this e-mail was sent to you in error and the
>>>> > e-mail
>>>> > contains patient information, please contact the Partners Compliance
>>>> > HelpLine at
>>>> > http://www.partners.org/complianceline . If the e-mail was sent to
>>>> you in
>&g

Re: [Freesurfer] Visualising regional values on the surface

[Kirstie Whitaker]

Thank you Michael! I <3 Pysurfer.

(and freesurfer of course!)

The *real* goal is to integrate the code that I've written as a wrapper
around pysurfer to show regional values (exactly as you suggest) with
BrainNet <https://www.nitrc.org/projects/bnv/> which can show the network
nicely on top of freesurfer files.

Here's the wiki for my pysurfer wrapper:
https://github.com/KirstieJane/DESCRIBING_DATA/wiki/Making-Surface-Plots-with-Pysurfer

And the code itself
https://github.com/KirstieJane/DESCRIBING_DATA/blob/master/VISUALIZING_SURFACE_MRI_DATA/pysurfer_plot_500parcellation_surface_values.py

Unfortunately I don't use BrainNet so I'm having difficulty helping my lab
mate make his pretty plots of network nodes and edges overlayed on top of
surface colors (eg: modular partition)!

Is there a way of writing out an annot file from pysurfer into freesurfer
format? Maybe that would bring the two packages closer together

Kx





On 29 March 2016 at 16:29, Michael Waskom <mwas...@stanford.edu> wrote:

> Hi Kirstie,
>
> Here's an example of how to do this in PySurfer:
> http://pysurfer.github.io/examples/plot_parc_values.html
>
> Hope that helps,
> Michael
>
> On Tue, Mar 29, 2016 at 8:08 AM, dgw <dgwake...@gmail.com> wrote:
>
>> Hi Kirstie,
>>
>> You could write your own CLUT file with the color corresponding to the
>> correlation you want to show?
>> Just open up the file and play with the values in the color columns.
>> Then simply load the color table in Freeview and use it to visualize
>> the annotation.
>>
>> There are of course other ways, but this is probably the quickest.
>>
>> hth
>> d
>>
>>
>> On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker <kw...@cam.ac.uk>
>> wrote:
>> > Hi,
>> >
>> > I'd like to show correlation coefficients by region on the brain
>> surface. So
>> > for example, if I've calculated a modular decomposition in a network
>> > analysis for each region of the D-K atlas I'd like to be able to color
>> each
>> > atlas region according to the module it has been assigned to.
>> >
>> > It seems like I have to do something with the ?h.aparc.annot files and a
>> > colour lookup table but I'm not sure exactly what.
>> >
>> > Thank you!
>> > Kx
>> >
>> > --
>> > Kirstie Whitaker, PhD
>> > Research Associate
>> >
>> > Department of Psychiatry
>> > University of Cambridge
>> >
>> > Mailing Address
>> > Brain Mapping Unit
>> > Department of Psychiatry
>> > Sir William Hardy Building
>> > Downing Street
>> > Cambridge CB2 3EB
>> >
>> > Phone: +44 7583 535 307
>> > Website: www.kirstiewhitaker.com
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to you
>> in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
>
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>


-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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[Freesurfer] Visualising regional values on the surface

[Kirstie Whitaker]

Hi,

I'd like to show correlation coefficients by region on the brain surface.
So for example, if I've calculated a modular decomposition in a network
analysis for each region of the D-K atlas I'd like to be able to color each
atlas region according to the module it has been assigned to.

It seems like I have to do something with the ?h.aparc.annot files and a
colour lookup table but I'm not sure exactly what.

Thank you!
Kx

-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

[Kirstie Whitaker]

I think eroding the region makes sense in general - you just have to be careful 
to exclude subjects who end up with no data (as you discovered!)

You could also look into why these three subjects had such small wm regions 
under entorhinal cortex. My (still) suspicious mind wonders if there is a bad 
reconstruction that is cutting out part of the inferior temporal lobe and 
therefore "squeezing" all of the cortical labels into a smaller volume. This 
would in turn give very small wm volumes.

On the other hand, entorhinal cortex may just have a relatively small amount of 
white matter underlying it because it's so "narrow" such that when you erode by 
1mm you are left with nothing for these three subjects.

Glad you figured out the odd correlations!

Kx

Sent from my iPhone, please excuse any typos or excessive brevity

> On 25 Mar 2016, at 01:22, Elijah Mak  wrote:
> 
> Hi Kirstie,
> 
> Yes indeed there were 3 subjects at the bottom-left of the plot. 
> 
> To account for PV, I eroded the boundaries using -seg-erode 1 during the 
> mri_segstats stage, and this resulted in a few subjects with no data for the 
> WM entorhinal region (although these were saved as "0" in the .stats file). 
> Do people generally do this for DTI studies?
> 
> All good now. 
> 
> Many thanks again, Kirstie.
> 
> Best Wishes,
> Elijah
> 
> 
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Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

[Kirstie Whitaker]

Hi Elijah,

Is there any chance you could attach a scatter plot? My suspicious mind thinks 
either a) there are outliers who are doing odd things, or b) the FA values are 
very different to those in other regions and therefore the correlation with MD 
wouldn't be expected to be the same. 

Kx

Sent from my iPhone, please excuse any typos or excessive brevity

> On 24 Mar 2016, at 23:59, Elijah Mak  wrote:
> 
> Hi Alshikho,
> 
> Yes, I am sure :) Same sequence for everyone. 
> 
> Just to add. FA and MD were significantly negatively correlated for the other 
> regions including the fusiform, precuneus, hippocampus, thalamus, etc. 
> 
> So I am very curious about what could be going on with the ERC here?
> 
> Best Wishes,
> Elijah
> 
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[Freesurfer] Postdoc job: Neuroimaging of mood disorders in adolescence at University of Cambridge

[Kirstie Whitaker]

Dear FSL, Freesurfer and Neuroimaging in Python list members (with
apologies for cross posting),

The closing date for this position is this SUNDAY 20th MARCH, so you don't
have much time (although we only need a cover letter and CV type details
for your application), but I've been asked to reach out to you because we'd
really like to hire the very best postdoc for this role at the University
of Cambridge. Please share this email widely with your personal and
professional networks.

The successful applicant will join a multidisciplinary team of scientists
investigating the neural basis and cognitive correlates of behavioural
phenotypes in large existing and still being collected longitudinal
community and clinical cohorts of adolescents and young adults as part of
the Neuroscience in Psychiatry Network (http://nspn.org.uk).

Applicants will have a PhD and some postdoctoral experience reflecting an
expert level of knowledge in cognitive and behavioural neuroscience
together with a working knowledge and interest in longitudinal data
analysis and mental illness.

The full job advert and instructions on how to apply are at
http://www.jobs.cam.ac.uk/job/9696.
The role comes with an invitation to interview for a fellowship at
Peterhouse, the oldest remaining college in Cambridge.

The start date is (reasonably) flexible but projected for May 2016. The
funds for this post are available until 31 March 2018 in the first instance.

The Clinical School at the University of Cambridge is a proud holder
of an Athena
SWAN Silver award <http://athena-swan.medschl.cam.ac.uk/> and candidates
from groups that are under-represented in senior STEMM positions (such as
women and people of colour) are particularly encouraged to apply.

If you have any informal questions about this vacancy please contact
Professor Ian Goodyer (ig...@cam.ac.uk)

For information on the application process for this vacancy, please contact
Dominic Drane, HR Administrator via email on
hradminpsychia...@medschl.cam.ac.uk.

Please quote reference RN08523 on your application and in any
correspondence about this vacancy.
Thank you
Kirstie Whitaker

-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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Re: [Freesurfer] group mean greater than X

[Kirstie Whitaker]

Could you also just subtract 5 from all your input data? Then when you test
against zero (and only look at positive p values) you'll really be testing
whether the values are greater than 5?

Kx

On 11 November 2015 at 21:35, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> I guess you could subtract 5 from the gamma.mgh, then recompute the t =
> gamma-5.mgh/sqrt(gammavar.mgh). You'd then need to convert the t to a p
> or sig given the dof.
> doug
>
> ps. Please remember to include previous correspondences so we know the
> context of the question
>
> On 11/11/15 4:10 PM, Dace Apshvalka wrote:
> > Sorry, I was not very clear.
> >
> > I meant, how do I test whether the group mean is greater than 5, for
> > example.
> >
> > The default is 0, but can I change it somehow?
> >
> >
> > Dace
>
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>
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-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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Re: [Freesurfer] Visualising surfaces at different fractional depths

[Kirstie Whitaker]

Thank you - right as you sent your reply I was writing an apology because
I'd just seen that flag.

It's Friday evening here in the UK and it might be time to stop sending
emails for a little while!

So sorry! And thank you!
Kx

On 24 April 2015 at 18:33, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Kirstie

 you can pick the interpolation method with

 --interp string

 where string is one of:

 nearest
 trilinear
 sinc
 cubic



 cheers
 Bruce
 On Fri, 24 Apr 2015, Kirstie Whitaker wrote:

  I'm sorry, I did wonder if my email wasn't clear as soon as I clicked
 send.

 I'm using mri_vol2surf and I've read the --help output and this page:
 https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf

 The help is very clear about which surface the volume is being sampled to
 etc, but I can't see a section that describes exactly how the values are
 interpolated (if they're interploated) onto the surface.

 The assumption that I was trying to clarify in my (too short) email was
 that
 the voxel through which the vertex passes is the value that is mapped to
 that vertex.

 Possible alternatives would be some sort of weighted sum of the
 neighboring
 voxels, perhaps, but I had assumed that if there were interpolations
 happening it would be mentioned in the help file?

 Does this make sense? I do apologise if I've missed an obvious reference
 that explains all this!

 Best wishes

 Kx


 On 24 April 2015 at 17:38, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
   Hi Kirstie

   I think you get to decide how you want the sampling done in
   mri_vol2surf.

   cheers
   Bruce
   On Fri, 24 Apr 2015, Kirstie Whitaker wrote:

 Thank you Bruce - that's excellent and works
 perfectly.

 Can I ask - when I sample from the new surface from
 a volume is it the voxel
 value in which the vertex lands that is assigned to
 the vertex or is there
 any interpolation across multiple voxels before
 assigning the vertex a
 value?

 Thanks again for the help!
 Kx

 On 20 April 2015 at 14:46, Bruce Fischl
 fis...@nmr.mgh.harvard.edu wrote:
   Hi Kirstie

   you can do this with mris_expand. For example:

   mris_expand -thickness lh.white 0.5 lh.graymid

   will generate a surface halfway between white
 and pial. Using
   that surface
   to sample is probably a better method than
 using profrac,
   although I expect
   the differences will be  small unless you have
 very highres
   data.

   cheers
   Bruce



   On Mon, 20 Apr 2015, Kirstie
   Whitaker wrote:

Hi experts,
   
I've used the command mri_vol2surf with the
 --projfrac 0.5
   flag to sample a
volume halfway between the pial and white
 matter surfaces.
   
I was wondering if there was a way to
 visualise where this
   surface lay on
the volume? Ideally I'd like to show a
 figure with the pial,
   white and this
halfway surface overlayed on the volume.
   
Any ideas?
   
Thank you
Kirstie
   
--
Kirstie Whitaker, PhD
Research Associate
   
Department of Psychiatry
University of Cambridge
   
Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB
   
Phone: +44 7583 535 307
Website: www.kirstiewhitaker.com
   
   
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 e-mail
 contains patient information, please contact the
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 HelpLine at
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 in error

Re: [Freesurfer] Visualising surfaces at different fractional depths

[Kirstie Whitaker]

Thank you Bruce - that's excellent and works perfectly.

Can I ask - when I sample from the new surface from a volume is it the
voxel value in which the vertex lands that is assigned to the vertex or is
there any interpolation across multiple voxels before assigning the vertex
a value?

Thanks again for the help!
Kx

On 20 April 2015 at 14:46, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Kirstie

 you can do this with mris_expand. For example:

 mris_expand -thickness lh.white 0.5 lh.graymid

 will generate a surface halfway between white and pial. Using that surface
 to sample is probably a better method than using profrac, although I expect
 the differences will be  small unless you have very highres data.

 cheers
 Bruce



 On Mon, 20 Apr 2015, Kirstie
 Whitaker wrote:

  Hi experts,
 
  I've used the command mri_vol2surf with the --projfrac 0.5 flag to
 sample a
  volume halfway between the pial and white matter surfaces.
 
  I was wondering if there was a way to visualise where this surface lay on
  the volume? Ideally I'd like to show a figure with the pial, white and
 this
  halfway surface overlayed on the volume.
 
  Any ideas?
 
  Thank you
  Kirstie
 
  --
  Kirstie Whitaker, PhD
  Research Associate
 
  Department of Psychiatry
  University of Cambridge
 
  Mailing Address
  Brain Mapping Unit
  Department of Psychiatry
  Sir William Hardy Building
  Downing Street
  Cambridge CB2 3EB
 
  Phone: +44 7583 535 307
  Website: www.kirstiewhitaker.com
 
 
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 The information in this e-mail is intended only for the person to whom it
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 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.




-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Visualising surfaces at different fractional depths

[Kirstie Whitaker]

I'm sorry, I did wonder if my email wasn't clear as soon as I clicked send.

I'm using mri_vol2surf and I've read the --help output and this page:
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2surf

The help is very clear about which surface the volume is being sampled to
etc, but I can't see a section that describes exactly how the values are
interpolated (if they're interploated) onto the surface.

The assumption that I was trying to clarify in my (too short) email was
that the voxel through which the vertex passes is the value that is mapped
to that vertex.

Possible alternatives would be some sort of weighted sum of the neighboring
voxels, perhaps, but I had assumed that if there were interpolations
happening it would be mentioned in the help file?

Does this make sense? I do apologise if I've missed an obvious reference
that explains all this!

Best wishes

Kx

On 24 April 2015 at 17:38, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Kirstie

 I think you get to decide how you want the sampling done in mri_vol2surf.

 cheers
 Bruce

 On Fri, 24 Apr 2015, Kirstie Whitaker wrote:

  Thank you Bruce - that's excellent and works perfectly.

 Can I ask - when I sample from the new surface from a volume is it the
 voxel
 value in which the vertex lands that is assigned to the vertex or is there
 any interpolation across multiple voxels before assigning the vertex a
 value?

 Thanks again for the help!
 Kx

 On 20 April 2015 at 14:46, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
   Hi Kirstie

   you can do this with mris_expand. For example:

   mris_expand -thickness lh.white 0.5 lh.graymid

   will generate a surface halfway between white and pial. Using
   that surface
   to sample is probably a better method than using profrac,
   although I expect
   the differences will be  small unless you have very highres
   data.

   cheers
   Bruce



   On Mon, 20 Apr 2015, Kirstie
   Whitaker wrote:

Hi experts,
   
I've used the command mri_vol2surf with the --projfrac 0.5
   flag to sample a
volume halfway between the pial and white matter surfaces.
   
I was wondering if there was a way to visualise where this
   surface lay on
the volume? Ideally I'd like to show a figure with the pial,
   white and this
halfway surface overlayed on the volume.
   
Any ideas?
   
Thank you
Kirstie
   
--
Kirstie Whitaker, PhD
Research Associate
   
Department of Psychiatry
University of Cambridge
   
Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB
   
Phone: +44 7583 535 307
Website: www.kirstiewhitaker.com
   
   
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 The information in this e-mail is intended only for the person to whom
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 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
 in error
 but does not contain patient information, please contact the sender
 and properly
 dispose of the e-mail.




 --
 Kirstie Whitaker, PhD
 Research Associate

 Department of Psychiatry
 University of Cambridge

 Mailing Address
 Brain Mapping Unit
 Department of Psychiatry
 Sir William Hardy Building
 Downing Street
 Cambridge CB2 3EB

 Phone: +44 7583 535 307
 Website: www.kirstiewhitaker.com


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 The information in this e-mail is intended only for the person to whom it
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 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.




-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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[Freesurfer] Visualising surfaces at different fractional depths

[Kirstie Whitaker]

Hi experts,

I've used the command mri_vol2surf with the --projfrac 0.5 flag to sample a
volume halfway between the pial and white matter surfaces.

I was wondering if there was a way to visualise where this surface lay on
the volume? Ideally I'd like to show a figure with the pial, white and this
halfway surface overlayed on the volume.

Any ideas?

Thank you
Kirstie

-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_vol2surf --prodist measuring from pial surface

[Kirstie Whitaker]

Thank you, Doug.

Can I just check that projdist is the same as projabs but with a different
name?

Just in case I'm using an old/wrong version, here's the last line from the
mri_vol2surf help output:
 $Id: mri_vol2surf.c,v 1.63 2011/03/05 01:11:14 jonp Exp $

From that help and your email I'm looking to run:

mri_vol2surf --mov input_volume \
--o $output_name \
--projdist -2 \
--interp nearest \
--surf pial \
--hemi lh

Which will give me values that are 2mm toward white matter from the pial
surface.

Thanks again for all the help!
Kx


On 3 December 2014 at 04:48, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:


 You can spec the surface to be pial (instead of the default white). Then
 spec --projabs to specify the distance into cortex (using negative numbers).
 doug


 On 11/27/14 1:24 PM, Kirstie Whitaker wrote:

  Hi,

 I was wondering if it's possible to sample x mm from the pial surface
 using mri_vol2surf (or another tool!). The point is that I'd like to be
 agnostic about exactly where the grey/white matter boundary lies.

  I've had a look through the help for mri_vol2surf and nothing's jumping
 out at me, is there an obvious option I'm missing?!

  Thank you!
 Kx


 --
  Kirstie Whitaker, PhD
 Research Associate

 Department of Psychiatry
 University of Cambridge

 *Mailing Address*
 Brain Mapping Unit
 Department of Psychiatry
 Sir William Hardy Building
 Downing Street
 Cambridge CB2 3EB

 *Phone: *+44 7583 535 307
  *Website:* www.kirstiewhitaker.com


 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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 The information in this e-mail is intended only for the person to whom it
 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.




-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_vol2surf --prodist measuring from pial surface

[Kirstie Whitaker]

Sorry - if anyone's looking at this in the future, you also need
--regheader subID in the command:

mri_vol2surf --mov input_volume \
--o $output_name \
--projdist -2 \
--interp nearest \
--surf pial \
--hemi lh \
--regheader subid

Kx



On 4 December 2014 at 20:41, Kirstie Whitaker kw...@cam.ac.uk wrote:

 Thank you, Doug.

 Can I just check that projdist is the same as projabs but with a different
 name?

 Just in case I'm using an old/wrong version, here's the last line from the
 mri_vol2surf help output:
  $Id: mri_vol2surf.c,v 1.63 2011/03/05 01:11:14 jonp Exp $

 From that help and your email I'm looking to run:

 mri_vol2surf --mov input_volume \
 --o $output_name \
 --projdist -2 \
 --interp nearest \
 --surf pial \
 --hemi lh

 Which will give me values that are 2mm toward white matter from the pial
 surface.

 Thanks again for all the help!
 Kx


 On 3 December 2014 at 04:48, Douglas Greve gr...@nmr.mgh.harvard.edu
 wrote:


 You can spec the surface to be pial (instead of the default white). Then
 spec --projabs to specify the distance into cortex (using negative numbers).
 doug


 On 11/27/14 1:24 PM, Kirstie Whitaker wrote:

  Hi,

 I was wondering if it's possible to sample x mm from the pial surface
 using mri_vol2surf (or another tool!). The point is that I'd like to be
 agnostic about exactly where the grey/white matter boundary lies.

  I've had a look through the help for mri_vol2surf and nothing's jumping
 out at me, is there an obvious option I'm missing?!

  Thank you!
 Kx


 --
  Kirstie Whitaker, PhD
 Research Associate

 Department of Psychiatry
 University of Cambridge

 *Mailing Address*
 Brain Mapping Unit
 Department of Psychiatry
 Sir William Hardy Building
 Downing Street
 Cambridge CB2 3EB

 *Phone: *+44 7583 535 307
  *Website:* www.kirstiewhitaker.com


 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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 The information in this e-mail is intended only for the person to whom it
 is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you
 in error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.




 --
 Kirstie Whitaker, PhD
 Research Associate

 Department of Psychiatry
 University of Cambridge

 *Mailing Address*
 Brain Mapping Unit
 Department of Psychiatry
 Sir William Hardy Building
 Downing Street
 Cambridge CB2 3EB

 *Phone: *+44 7583 535 307
 *Website:* www.kirstiewhitaker.com




-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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[Freesurfer] mri_vol2surf --prodist measuring from pial surface

[Kirstie Whitaker]

Hi,

I was wondering if it's possible to sample x mm from the pial surface using
mri_vol2surf (or another tool!). The point is that I'd like to be agnostic
about exactly where the grey/white matter boundary lies.

I've had a look through the help for mri_vol2surf and nothing's jumping out
at me, is there an obvious option I'm missing?!

Thank you!
Kx


-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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[Freesurfer] Appropriate levels of surface smoothing

[Kirstie Whitaker]

Hi everyone,

Firstly - thank you for the excellent tools. This year has been my first
foray into surfaced based analysis and I'm enjoying it very much.

I don't currently have a gut instinct for an appropriate level of surface
smoothing. I'm sure that can't be easily answered but would a range of,
say, 3 to 5mm sound good? Or more like 10 to 15mm?

Currently I'm considering cortical thickness analyses, but I may extend
into functional analyses in the future.

If there are any references that you can recommend I'd appreciate that very
much.

Best wishes
Kirstie

-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

*Mailing Address*
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building
Downing Street
Cambridge CB2 3EB

*Phone: *+44 7583 535 307
*Website:* www.kirstiewhitaker.com
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[Freesurfer] tracula update link not working

[Kirstie Whitaker]

Hi,

I apologise if this is only on my end but I can't seem to download any of the 
updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was successful 
last week so I wonder if something's changed?

Thanks
Kx

-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building 
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307
Website: www.kirstiewhitaker.com
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Re: [Freesurfer] tracula update link not working

[Kirstie Whitaker]

Yep! Working now - thank you very much :)

Kx


 On 20 August 2014 12:23, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu 
 wrote:
 
 Hi Kirstie - This was a glitch related to yesterday's storage cluster
 maintence. It's been fixed now, so please try again.
 
 a.y
 
 On Wed, 20 Aug 2014, Kirstie Whitaker wrote:
 
  Hi,
 
  I apologise if this is only on my end but I can't seem to download any of 
  the updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was 
  successful last week
  so I wonder if something's changed?
 
  Thanks
  Kx
 
  --
  Kirstie Whitaker, PhD
  Research Associate
 
  Department of Psychiatry
  University of Cambridge
 
  Mailing Address
  Brain Mapping Unit
  Department of Psychiatry
  Sir William Hardy Building
  Downing Street
  Cambridge CB2 3EB
 
  Phone: +44 7583 535 307
  Website: www.kirstiewhitaker.com
 
 
 ___
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the e-mail
 contains patient information, please contact the Partners Compliance HelpLine 
 at
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
 error
 but does not contain patient information, please contact the sender and 
 properly
 dispose of the e-mail.



-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building 
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307
Website: www.kirstiewhitaker.com
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[Freesurfer] Some notes on getting Tracula to work for newbies

[Kirstie Whitaker]

Hi Anastasia and the freesurfer list,

I've been working on getting the latest version of tracula to run and I thought 
I would post here the errors that I've worked around. It's all been based on 
looking through the mailing list archives but I thought it would be useful to 
add them here all in one place! The goal of this email is simply to save time 
for others in the future (including myself when I forget all these things!)

[Note that if I've written something between   then it will be specific to 
your files/directories etc]

When running trac-all on an input nii file with corresponding bval and bvec 
files:

1) If you're getting an error that says:

nifti1Read(): unsupported slice timing pattern 5 in NAME OF YOUR DTI NIFTI 
FILE

Try running the command:

fslmaths NAME OF YOUR DTI NIFTI FILE NAME OF YOUR DTI NIFTI FILE

eg: fslmaths dti.nii.gz dti.nii.gz

I'm really not clear on what exactly is wrong with my files (created using an 
in house dicom converter) but taking in the file and writing it straight back 
out again gets rid of this problem for me.

2) If you're getting an error that says

ERROR: Could not open SUBJECTS_DIR/SUBID/dmri/bvals for reading

Then you're probably using the centos4 update at 
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two options - if the 
centos6 update works then switch to that, otherwise all other steps in trac-all 
-prep work *except* for the quality control. So you can run trac-all -prep 
-noqa and all should be well.

To install the update just download it (I used wget TRACULA_UPDATE_LINK) and 
the untar it (tar -zxvf TRACULA_UPDATE_TAR.GZ_FILE). Copy the files inside 
the folder you've created into the $FREESURFER_HOME/bin/ directory.

3) If you're getting an error that says (something along the lines of)

mri_convert --frame 0 14 27 41 54 68 SUBJECTS_DIR/SUBID/dmri/dwi.nii.gz 
SUBJECTS_DIR/SUBID/dmri/lowb.nii.gz

mri_convert: extra arguments (41 and following)

type mri_convert -u for usage

Then you're probably using an old version of trac-all. Double check that you've 
replaced the appropriate files in your $FREESURFER_HOME/bin directory with 
those contained in the appropriate update at 
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. (See my instructions at point 
2).


Some fun facts from my experience:
You can have decimal points (not commas though) in your bvals files.
You can run trac-all in either a bash or tcsh shell.
(These were not the droids I was looking for)

Thanks again for the really excellent software. And please correct anything 
that I've written here if it's wrong!

Kx

-- 
Kirstie Whitaker, PhD
Research Associate

Department of Psychiatry
University of Cambridge

Mailing Address
Brain Mapping Unit
Department of Psychiatry
Sir William Hardy Building 
Downing Street
Cambridge CB2 3EB

Phone: +44 7583 535 307
Website: www.kirstiewhitaker.com
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Re: [Freesurfer] Some notes on getting Tracula to work for newbies

[Kirstie Whitaker]

On 20 August 2014 14:27, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
wrote:


 Thanks a lot, Kirstie. Nice job on finding solutions in the archives! You
 are a model user :)


Thank youalthough unfortunately not quite the best user - I still have
problems...

I think I lied in my earlier email - I think that the mri_convert problem
(#3 below) is actually in the newest version of trac-preproc. (I didn't do
a great job of keeping track of my version because I was being lazy! More
fool me.)

Here's the part of the code which in the May 2014 update ('$Id:
trac-preproc,v 1.49 2014/03/22 03:31:22 ayendiki Exp $' ) that is leading
to the error:

#=
  # Make diffusion brain mask
  if ($#nb0  0) then
set lowblist = ()
@ k = 0
while ($k  $nb0)
  set lowblist = ($lowblist $k)
  @ k = $k + 1
end
  else
set bmin = `grep -v ^$ $dwidir/dwi_orig.mghdti.bvals \
| sort --numeric-sort | head -1`
set lowblist = `cat $dwidir/dwi_orig.mghdti.bvals \
| awk -v bmin=$bmin '{if ($1 == bmin) print NR-1}'`
  endif

  if (! $#lowblist) then
echo ERROR: Cannot detect low-b volumes
goto error_exit
  endif

  set cmd = mri_convert
  set cmd = ($cmd --frame $lowblist)
  set cmd = ($cmd $dwidir/dwi.nii.gz)
  set cmd = ($cmd $dwidir/lowb.nii.gz)
  echo $cmd | tee -a $LF | tee -a $CF
  if ($RunIt) then
$cmd | tee -a $LF
if ($status) goto error_exit
  endif

#=

Which leads to this command:

 mri_convert --frame 0 14 27 41 54 68
/scratch/kw401/UCHANGE_INTERIM/SUB_DATA/10778/SURFER/MRI0/dmri/dwi.nii.gz
/scratch/kw401/UCHANGE_INTERIM/SUB_DATA/10778/SURFER/MRI0/dmri/lowb.nii.gz

And then to this error:

 mri_convert: extra arguments (41 and following)


I made the following changes to the code (trac-preproc) and everything
seems to run just fine.

#=
OLD
  set cmd = ($cmd --frame $lowblist)

NEW
 set cmd = ($cmd --frame ${lowblist[1]})

#=

What do you think? Is this just an odd-ness for me, or is it a helpful fix?
One thing that I haven't been able to ascertain is whether I have an old
version of mri_convert that should be able to concatenate the six listed
volumes! (The next section of code seems to look like its trying to
concatenate volumes so it might be expecting a 4D file? Or multiple
lowb.nii.gz volumes?)

I hope this all makes sense! Thank you again for all your hard work!
Kx



 On Wed, 20 Aug 2014, Kirstie Whitaker wrote:

  Hi Anastasia and the freesurfer list,
 
  I've been working on getting the latest version of tracula to run and I
 thought I would post here the errors that I've worked around. It's all been
 based on looking
  through the mailing list archives but I thought it would be useful to
 add them here all in one place! The goal of this email is simply to save
 time for others in the
  future (including myself when I forget all these things!)
 
  [Note that if I've written something between   then it will be
 specific to your files/directories etc]
 
  When running trac-all on an input nii file with corresponding bval and
 bvec files:
 
  1) If you're getting an error that says:
 
  nifti1Read(): unsupported slice timing pattern 5 in NAME OF YOUR DTI
 NIFTI FILE
 
  Try running the command:
 
  fslmaths NAME OF YOUR DTI NIFTI FILE NAME OF YOUR DTI NIFTI FILE
 
  eg: fslmaths dti.nii.gz dti.nii.gz
 
  I'm really not clear on what exactly is wrong with my files (created
 using an in house dicom converter) but taking in the file and writing it
 straight back out again
  gets rid of this problem for me.
 
  2) If you're getting an error that says
 
  ERROR: Could not open SUBJECTS_DIR/SUBID/dmri/bvals for reading
 
  Then you're probably using the centos4 update at
 http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two options -
 if the centos6 update works then switch to
  that, otherwise all other steps in trac-all -prep work *except* for the
 quality control. So you can run trac-all -prep -noqa and all should be well.
 
  To install the update just download it (I used wget
 TRACULA_UPDATE_LINK) and the untar it (tar -zxvf
 TRACULA_UPDATE_TAR.GZ_FILE). Copy the files inside the folder
  you've created into the $FREESURFER_HOME/bin/ directory.
 
  3) If you're getting an error that says (something along the lines of)
 
  mri_convert --frame 0 14 27 41 54 68
 SUBJECTS_DIR/SUBID/dmri/dwi.nii.gz
 SUBJECTS_DIR/SUBID/dmri/lowb.nii.gz
 
  mri_convert: extra arguments (41 and following)
 
  type mri_convert -u for usage
 
  Then you're probably using an old version of trac-all. Double check that
 you've replaced the appropriate files in your $FREESURFER_HOME/bin
 directory with those
  contained in the appropriate update at
 http

[Freesurfer] Destrieux atlas in FSL

[Kirstie Whitaker]

Hi Freesurfer and FSL communities,

Firstly, I apologise for the double posting. I suspect there are experts in
both groups that can help me.

I'd like to be able to visualise the Destrieux atlas that freesurfer uses
at the same time as my MNI standard space results in FSL.

Is that possible? I'm afraid I've not been successful in my search of the
mailing list archives.

Thank you for your help.

Kirstie

-- 
Kirstie Whitaker, PhD
Research Associate

tel: +44 7583 535 307

Department of Psychiatry
University of Cambridge
Herchel Smith Building
Robinson Way
Cambridge CB2 0SZ
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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.