Re: [Freesurfer] Parcellation labels error

[Ali,Mohamed Tarek Mohamed]

External Email - Use Caution

Nope, but Based on the ctable every region has an ID, something like "632550" 
but sometimes when I read the lh.aparc.annot using matlab, I read labels values 
equal to 0, which has no match in the ctable.

I don't understand if these zeros represent an unknown area, or is it a bug?


I assign all vertices, with label values equal to zeros, to the unknown region, 
however, the unknown region already has a label value in the ctable. That's 
what I don't understand


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, August 27, 2018 2:36:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Parcellation labels error

was there something other than CC that had 0 number of verts?

b'unknown' contains: 6695
b'insula' contains: 3551
b'temporalpole' contains: 552
b'precuneus' contains: 5189
b'frontalpole' contains: 351
b'transversetemporal' contains: 695
b'supramarginal' contains: 5915
b'superiorfrontal' contains: 9823
b'superiortemporal' contains: 5738
b'parstriangularis' contains: 2286
b'rostralmiddlefrontal' contains: 7656
b'medialorbitofrontal' contains: 2167
b'isthmuscingulate' contains: 1359
b'superiorparietal' contains: 7060
b'lateraloccipital' contains: 7440
b'lateralorbitofrontal' contains: 3510
b'fusiform' contains: 4661
b'posteriorcingulate' contains: 1783
b'inferiorparietal' contains: 6607
b'parahippocampal' contains: 965
b'caudalanteriorcingulate' contains: 779
b'parsopercularis' contains: 2422
b'rostralanteriorcingulate' contains: 853
b'precentral' contains: 6554
b'lingual' contains: 3628
b'postcentral' contains: 6424
b'bankssts' contains: 1613
b'corpuscallosum' contains: 0
b'paracentral' contains: 2045
b'parsorbitalis' contains: 936
b'entorhinal' contains: 458
b'caudalmiddlefrontal' contains: 2994
b'pericalcarine' contains: 1564
b'inferiortemporal' contains: 5501
b'middletemporal' contains: 5220
b'cuneus' contains: 2000



On 08/27/2018 12:09 PM, Ali,Mohamed Tarek Mohamed wrote:
>
> External Email - Use Caution
>
> and what about the 0's showing up in labels?
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Douglas N. Greve
> 
> *Sent:* Monday, August 27, 2018 11:04:01 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Parcellation labels error
> Neither the aparc nor the aparc.DKTatlas have corpus callosum labeled.
> It is labled in the aseg.mgz though
>
> On 08/27/2018 10:24 AM, Ali,Mohamed Tarek Mohamed wrote:
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> >
> > While I am using [vec,labels,cnames] =
> > read_annotation('lh.aparc.annot'), I am getting values in labels which
> > are not found in cnames.table(:,5). These values are 0. I assigned the
> > values to the unknown area. However, when I looked at the number of
> > vertices per brain regions I found that corpuscallosum has no vertices
> > in the DK atlas.
> >
> >
> > This is my first week using a neuroimaging software and Freesurfer is
> > my first software to work on, so I just don't know if that's ok or if
> > there is something wrong.
> >
> >
> > I am attaching the output of a python code I wrote to count the number
> > of vertices per brain region in the left hemisphere of a structural
> > MRI image from our dataset.
> >
> >
> > Thanks in advance,
> >
> > *Mohamed T. Ali*
> >
> > *Ph.D. student,
> > Bioengineering,*
> >
> > *University of Louisville.*
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIF-g=OAG1LQNACBDguGvBeNj18Swhr9TMTjS-x4O_KuapPgY=rGLYk-ud8PYpVnuGAilySGbwhsnX9td8mB7-A6d-rlhl5PqJuRw4ipUJfvEXPCBj=xkejPwa1m44F37y_Hv-LJOoJq4TMZOuz9s3h74_1P5U=7RVcTv16gUezrl_klSj7OrVI5dLaWdtPPYdYzXw33XY=
>
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>
>
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> 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
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> . If the 

Re: [Freesurfer] Parcellation labels error

[Douglas N. Greve]

was there something other than CC that had 0 number of verts?

b'unknown' contains: 6695
b'insula' contains: 3551
b'temporalpole' contains: 552
b'precuneus' contains: 5189
b'frontalpole' contains: 351
b'transversetemporal' contains: 695
b'supramarginal' contains: 5915
b'superiorfrontal' contains: 9823
b'superiortemporal' contains: 5738
b'parstriangularis' contains: 2286
b'rostralmiddlefrontal' contains: 7656
b'medialorbitofrontal' contains: 2167
b'isthmuscingulate' contains: 1359
b'superiorparietal' contains: 7060
b'lateraloccipital' contains: 7440
b'lateralorbitofrontal' contains: 3510
b'fusiform' contains: 4661
b'posteriorcingulate' contains: 1783
b'inferiorparietal' contains: 6607
b'parahippocampal' contains: 965
b'caudalanteriorcingulate' contains: 779
b'parsopercularis' contains: 2422
b'rostralanteriorcingulate' contains: 853
b'precentral' contains: 6554
b'lingual' contains: 3628
b'postcentral' contains: 6424
b'bankssts' contains: 1613
b'corpuscallosum' contains: 0
b'paracentral' contains: 2045
b'parsorbitalis' contains: 936
b'entorhinal' contains: 458
b'caudalmiddlefrontal' contains: 2994
b'pericalcarine' contains: 1564
b'inferiortemporal' contains: 5501
b'middletemporal' contains: 5220
b'cuneus' contains: 2000



On 08/27/2018 12:09 PM, Ali,Mohamed Tarek Mohamed wrote:
>
> External Email - Use Caution
>
> and what about the 0's showing up in labels?
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N. Greve 
> 
> *Sent:* Monday, August 27, 2018 11:04:01 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Parcellation labels error
> Neither the aparc nor the aparc.DKTatlas have corpus callosum labeled.
> It is labled in the aseg.mgz though
>
> On 08/27/2018 10:24 AM, Ali,Mohamed Tarek Mohamed wrote:
> >
> > External Email - Use Caution
> >
> > Hello FreeSurfer Developers,
> >
> >
> > While I am using [vec,labels,cnames] =
> > read_annotation('lh.aparc.annot'), I am getting values in labels which
> > are not found in cnames.table(:,5). These values are 0. I assigned the
> > values to the unknown area. However, when I looked at the number of
> > vertices per brain regions I found that corpuscallosum has no vertices
> > in the DK atlas.
> >
> >
> > This is my first week using a neuroimaging software and Freesurfer is
> > my first software to work on, so I just don't know if that's ok or if
> > there is something wrong.
> >
> >
> > I am attaching the output of a python code I wrote to count the number
> > of vertices per brain region in the left hemisphere of a structural
> > MRI image from our dataset.
> >
> >
> > Thanks in advance,
> >
> > *Mohamed T. Ali*
> >
> > *Ph.D. student,
> > Bioengineering,*
> >
> > *University of Louisville.*
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIF-g=OAG1LQNACBDguGvBeNj18Swhr9TMTjS-x4O_KuapPgY=rGLYk-ud8PYpVnuGAilySGbwhsnX9td8mB7-A6d-rlhl5PqJuRw4ipUJfvEXPCBj=xkejPwa1m44F37y_Hv-LJOoJq4TMZOuz9s3h74_1P5U=7RVcTv16gUezrl_klSj7OrVI5dLaWdtPPYdYzXw33XY=
>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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>
>
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> 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 
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Re: [Freesurfer] correlation between blood biomarkers and longitudinal decrease in cortical thickness

[Martin Reuter]

Hi Foad, 

if all subjects have 2 time point and same time delta, you can compute the 
difference between time points, divide by 2 (for yearly change) and run a 
standard GLM analysis on that measure instead of thickness. 

Or you can model this with linear mixed effects models (which makes sense if 
time deltas are very different or if you have different many time points per 
subject). 

Best, Martin



> On 20. Aug 2018, at 22:27, Foad Taghdiri  
> wrote:
> 
>External Email - Use Caution
> 
> Hello,
> 
> I have done freesurfer (v6) longitudinal preprocessing for 20 subjects 
> (baseline and 2-year follow-up). We also have levels of some blood biomarkers 
> (e.g. tau, neurofilament light) for these subjects at the baseline. I am 
> interested to figure out if the level of blood biomarkers at the baseline is 
> related to the amount of cortical thinning over time, and if so, which brain 
> regions’ cortical thinning are significantly correlated with the blood 
> biomarker. I was wondering if you could please guide me through this analysis 
> and let me know how I can do it.
> 
> Thanks
> Best,
> Foad
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 


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Re: [Freesurfer] Parcellation labels error

[Ali,Mohamed Tarek Mohamed]

External Email - Use Caution

and what about the 0's showing up in labels?


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, August 27, 2018 11:04:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Parcellation labels error

Neither the aparc nor the aparc.DKTatlas have corpus callosum labeled.
It is labled in the aseg.mgz though

On 08/27/2018 10:24 AM, Ali,Mohamed Tarek Mohamed wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
>
> While I am using [vec,labels,cnames] =
> read_annotation('lh.aparc.annot'), I am getting values in labels which
> are not found in cnames.table(:,5). These values are 0. I assigned the
> values to the unknown area. However, when I looked at the number of
> vertices per brain regions I found that corpuscallosum has no vertices
> in the DK atlas.
>
>
> This is my first week using a neuroimaging software and Freesurfer is
> my first software to work on, so I just don't know if that's ok or if
> there is something wrong.
>
>
> I am attaching the output of a python code I wrote to count the number
> of vertices per brain region in the left hemisphere of a structural
> MRI image from our dataset.
>
>
> Thanks in advance,
>
> *Mohamed T. Ali*
>
> *Ph.D. student,
> Bioengineering,*
>
> *University of Louisville.*
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=DwIF-g=OAG1LQNACBDguGvBeNj18Swhr9TMTjS-x4O_KuapPgY=rGLYk-ud8PYpVnuGAilySGbwhsnX9td8mB7-A6d-rlhl5PqJuRw4ipUJfvEXPCBj=xkejPwa1m44F37y_Hv-LJOoJq4TMZOuz9s3h74_1P5U=7RVcTv16gUezrl_klSj7OrVI5dLaWdtPPYdYzXw33XY=

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Re: [Freesurfer] recon-all with mri_ca_normalize (longitudinal)

[Martin Reuter]

Hi Paul, 

you will need aseg and maybe more in the -long runs anyway. But if you really 
want to stop after norm

 … -autorecon1 -gcareg -canorm

passing autorecon2 will do the whole block : 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 


Best, Martin


> On 10. Aug 2018, at 18:01, miracle ozzoude  wrote:
> 
> External Email - Use Caution
> 
> 
> Hello FreeSurfer team, 
> 
> In order to create the longitudinal base after norm.mgz, Is the command below 
> the right way to end recon-all after creating norm.mgz? 
> 
> recon-all -s subjectID -autorecon1 -autorecon2  -i T1image -canorm. 
> 
> Thank you. 
> 
> Best, 
> Paul
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Re: [Freesurfer] Parcellation labels error

[Douglas N. Greve]

Neither the aparc nor the aparc.DKTatlas have corpus callosum labeled. 
It is labled in the aseg.mgz though

On 08/27/2018 10:24 AM, Ali,Mohamed Tarek Mohamed wrote:
>
> External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
>
> While I am using [vec,labels,cnames] = 
> read_annotation('lh.aparc.annot'), I am getting values in labels which 
> are not found in cnames.table(:,5). These values are 0. I assigned the 
> values to the unknown area. However, when I looked at the number of 
> vertices per brain regions I found that corpuscallosum has no vertices 
> in the DK atlas.
>
>
> This is my first week using a neuroimaging software and Freesurfer is 
> my first software to work on, so I just don't know if that's ok or if 
> there is something wrong.
>
>
> I am attaching the output of a python code I wrote to count the number 
> of vertices per brain region in the left hemisphere of a structural 
> MRI image from our dataset.
>
>
> Thanks in advance,
>
> *Mohamed T. Ali*
>
> *Ph.D. student,
> Bioengineering,*
>
> *University of Louisville.*
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Follow-Up: Longitudinal Processing - Retaining Manual Edits

[Martin Reuter]

Hi Kaley, 

the problem is,, when you re-run the base with different images, it will create 
the median image at a different location. That means that all your edits will 
be at the wrong location. I currently don’t see a way to fix this easily 
without a lot of tweaking of the recon-all script. One potential approach could 
be to manually create the new template with the correct images at the same 
location as before, by passing the old template into the mri_robust_template 
code as an initial target (not even sure there is a flag for that). Then start 
recon-all from a later stage after that. I cannot support you for this and it 
requires some coding skills and good knowledge of the individual steps in the 
base pipeline. 

Best, Martin



> On 31. Jul 2018, at 18:35, KALEY E ELLIS  wrote:
> 
> Dear FreeSurfer Developers,
>  
> I posted this question last week, but did not receive a response. Please let 
> me know if I can provide any additional information.
> 
> We are using your longitudinal processing pipeline (version 6.0) for our 
> study (n=140, 3 timepoints). Our scanner was upgraded a year ago and the  a 
> filter was used on the raw images to adjust for hyperintensities in the 
> images due to using a multi-channel coil. 
>  
> At this point, our bases have already been processed and consist of three 
> timepoints with a mix of filters: T1 no filter, T2 no filter, T3 with filter. 
> Since we have invested many resources into the manual editing process, we 
> want to try to retain all the manual edits that have been done to the base. 
> We still have the original scan and the filtered scan for each subject. We 
> have some ideas on how we might be able to retain the edits, but would you be 
> able to provide  input regarding whether this seems reasonable? Your feedback 
> is greatly appreciated!
>  
> Plan A:
> 1) Create a new T3 cross-sectional with the correct nifti
> 2) Run recon-all on the existing base
> Q: Will this retain the previous manual edits AND incorporate the new 
> cross-sectional image?
>  
> Plan B:
> 1) Create a new T3 cross-sectional with the correct nifti
> 2) Create a new base
> Q: Is it possible to transfer data from old manual edits to a new base? If 
> so, how?
> 
> Thank you!
> Kaley
> 
> Associate Research Specialist
> Center for Healthy Minds
> Waisman Center for Brain Imaging and Behavior
> University of Wisconsin-Madison
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> 
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Re: [Freesurfer] error with mri_ca_register in long

[Martin Reuter]

Hi Paul, 

Does this happen in the base or in the long step?

-bigventricle has never been tested within the long stream and this is bug that 
needs to be fixed at some point (assuming the big ventricle is supported in the 
next release )

We should put this on our known issues list. 

Best, Martin


> On 5. Jul 2018, at 18:23, miracle ozzoude  wrote:
> 
> External Email - Use Caution
> 
> 
> Hello All, 
> 
> When running the longitudinal pipeline for version 6, i encountered this 
> error " TransformSample: gcam has not been inverted!; Numerical result out of 
> range". I found a thread with similar error but the problem wasn't solved. 
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-April/051240.html 
> .
>  
> Just like the previous thread, it happens whenever I include the 
> "-bigventricle" flag. Below is a sample of my recon-all scripts from 
> cross-sectional to longitudinal. The error.log and recon.log files are too 
> large to send. Thank you. 
> 
> Best, 
> Paul
> 
> Cross-sectional
> recon-all -s ${SUBJECTS_DIR}/$session -autorecon-all -i ${filename} 
> -hippocampal-subfields-T1 -parallel -openmp 20 -bigventricles -3T -time
> 
> Longitudinal 
> recon-all -base ${session} -tp "${tp1}" -tp "${tp2}" -all -parallel -openmp 
> 20 -bigventricles -3T -time 
> 
> recon-all -long ${tp1} ${session} -all -parallel -openmp 20 -bigventricles 
> -3T -time
> recon-all -long ${tp2} ${session} -all -parallel -openmp 20 -bigventricles 
> -3T -time
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Re: [Freesurfer] Resample data for longitudinal comparisons

[Martin Reuter]

Hi James, 

I would not run upsampled data through the highres pipeline. (not even sure I 
would run highres data through that). 

So you should sample to 1mm resolution. To be fair you should also resample the 
1mm image to a new position (to also introduce interpolation artefacts there). 
You could use my make_upright script for that, which uses mri_robust_register 
to map the image to an upright and straight head position. 

Best, Martin


> On 20. Jul 2018, at 22:15, James Gullickson  wrote:
> 
> External Email - Use Caution
> 
> 
> All,
> 
> I would like to compare cortical thickness between two timepoints.
> 
> Timepoint 1 has 1mm^3 data.
> Timepoint 2 has 0.8mm^3 data.
> 
> I realize that there are limitations with this change in resolution between 
> timepoints and that no analysis is going to be perfect, but I am trying to 
> come up with the best possible solution.
> 
> Would it work to resample both timepoints' raw data into 0.9mm^3 ( 
> mri_convert --conform_size 0.9 invol outvol ), and then run the 0.9mm data 
> through Freesurfer 6.0 submilimeter recon? If so, are there any special 
> considerations I need to take into account after the initial recon, or would 
> longitudinal processing after this point be per normal?
> 
> Thanks,
> 
> James
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Re: [Freesurfer] Longitudinal Processing question

[Martin Reuter]

Hi Ryan, 

 FreeSurfers Longitudinal pipeline assumes head size is relatively fixed. The 
problem with growing heads is that the surfaces from the subject-template will 
not fit well to later (or earlier) time points and that the algorithm can 
potentially not recover. If surfaces look OK it means it worked. I have no idea 
how large the time delta is for it to fail but I guess if you scan a 4 year old 
and then again when they are 12 that could be problematic. 

You should use eTIV from the cross stream. In the long stream eTiv is fixed 
across time.


Best, Martin

> On 9. Jul 2018, at 20:51, Nillo, Ryan Michael R  
> wrote:
> 
>External Email - Use Caution
> 
> Hello FreeSurfer experts,
> 
> I have a few questions on the longitudinal processing stream. I am interested 
> in studying longitudinal morphometry changes in a pediatric population. The 
> age range of this population is between 4-20 years with age deltas between a 
> few months to < 2 years. I want to know what are appropriate/acceptable age 
> deltas used for longitudinal processing. I looked through the archives and 
> one researcher asked about age deltas. One of the answers was that “if the 
> time delta is relatively small, this has good chances to work”. What does 
> “relatively small” mean? If the time points exit the longitudinal pipeline 
> without errors and the surfaces look correct, does this mean the data is 
> relevant?? When I correct for head size, should I use the eTIV values from 
> the cross-sectional directories or the longitudinal directories?
> 
> Thanks in advance,
> 
> Ryan Michael Nillo
> Staff Research Associate I
> University of California San Francisco
> Department of Radiology and Biomedical Imaging
> 
> 
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> 
> 


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Re: [Freesurfer] Missingness and recent developments in longitudinal pipeline for pediatric samples

[Martin Reuter]

Hi Laurel and Johannes, 

Pediatric: if the time distance is small it should also work in paediatric 
images. You can just test it on a couple cases and if too many edits would be 
required, then simply use the cross sectional processed results.

There is no thorough analysis, but missingness is not a big problem if you use 
Linear Mixed Effects Modeling. You can even include subjects with a single time 
point (but make sure you run it also through the longitudinal stream so that 
that single image undergoes the same processing steps as the rest). 

Best, Martin

> On 9. Jul 2018, at 15:50, Mohn, Johannes  wrote:
> 
> 
> Dear FS Experts and Community,
>  
> we are working on a longitudinal dataset of structural T1w images in a 
> pediatric sample assessed at 2 waves, 2 years apart (aged 6/7 and 8/9).
> As far as we know, it is yet unresolved whether the Freesurfer longitudinal 
> pipeline is robust in pediatric samples, where the head size is still 
> changing or have there been any recent developments?
> Also, is there any documentation on how missingness affects this Pipeline?
>  
> We look forward to your response
>  
> Thank you,
>  
> Laurel and Johannes
>  
> Jacobs Entwicklungsstudie
>  
> Max-Planck-Institut für Bildungsforschung
> Max Planck Institute for Human Development
> Lentzeallee 94
> 14195 Berlin
>  
> Tel.: 030-824 06 371
> E-Mail: jacobs-stu...@mpib-berlin.mpg.de 
> 
>  
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> 
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Re: [Freesurfer] freesurfer development version for mac incomplete

[Hoopes, Andrew]

Hi Ani, are you using 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-darwin-OSX-ElCapitan-dev.tar.gz
 and are you sure the downloaded fully completed?

Best,
Andrew

From:  on behalf of Anik Dar 

Reply-To: FS Help 
Date: Monday, August 27, 2018 at 8:46 AM
To: FS Help 
Subject: [Freesurfer] freesurfer development version for mac incomplete


External Email - Use Caution
Hi

When I try to download the development version of freesurfer for mac, the file 
size is only 138 MB and doesnt unzip once downloaded.

Is there another link where the complete development version for mac can be 
found ?

Thanks

Ani
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Re: [Freesurfer] Seeing the Parcels as Volumes

[Douglas Greve]

Have you looked at aparc+aseg.mgz? You can change it to nii with 
mri_convert aparc+aseg.mgz aparc+aseg.nii



On 8/27/18 5:54 AM, Maedeh Khalilian wrote:


External Email - Use Caution

Dear FreeSurfer experts,
I have used "mri_annnotation2label" and "mri_label2vol" to change the 
parcellation output of FreeSurfer e.g the lh.aparc.annot into an 
".nii" so i can see the parcels in Mricro.

Now I can see the parcels just on the cortex not on the whole graymatter.
The first question I have is that, is the parcellation done on the 
whole graymatter?
And if yes, is there a way that I can see the volumes on the whole 
graymatter, not just on the cortex?

I would be grateful if you could help me.
best regards,
Maedeh,


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[Freesurfer] Parcellation labels error

[Ali,Mohamed Tarek Mohamed]

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Hello FreeSurfer Developers,


While I am using [vec,labels,cnames] = read_annotation('lh.aparc.annot'), I am 
getting values in labels which are not found in cnames.table(:,5). These values 
are 0. I assigned the values to the unknown area. However, when I looked at the 
number of vertices per brain regions I found that corpuscallosum has no 
vertices in the DK atlas.


This is my first week using a neuroimaging software and Freesurfer is my first 
software to work on, so I just don't know if that's ok or if there is something 
wrong.


I am attaching the output of a python code I wrote to count the number of 
vertices per brain region in the left hemisphere of a structural MRI image from 
our dataset.


Thanks in advance,

Mohamed T. Ali

Ph.D. student,
Bioengineering,

University of Louisville.
b'unknown' contains: 6695
b'insula' contains: 3551
b'temporalpole' contains: 552
b'precuneus' contains: 5189
b'frontalpole' contains: 351
b'transversetemporal' contains: 695
b'supramarginal' contains: 5915
b'superiorfrontal' contains: 9823
b'superiortemporal' contains: 5738
b'parstriangularis' contains: 2286
b'rostralmiddlefrontal' contains: 7656
b'medialorbitofrontal' contains: 2167
b'isthmuscingulate' contains: 1359
b'superiorparietal' contains: 7060
b'lateraloccipital' contains: 7440
b'lateralorbitofrontal' contains: 3510
b'fusiform' contains: 4661
b'posteriorcingulate' contains: 1783
b'inferiorparietal' contains: 6607
b'parahippocampal' contains: 965
b'caudalanteriorcingulate' contains: 779
b'parsopercularis' contains: 2422
b'rostralanteriorcingulate' contains: 853
b'precentral' contains: 6554
b'lingual' contains: 3628
b'postcentral' contains: 6424
b'bankssts' contains: 1613
b'corpuscallosum' contains: 0
b'paracentral' contains: 2045
b'parsorbitalis' contains: 936
b'entorhinal' contains: 458
b'caudalmiddlefrontal' contains: 2994
b'pericalcarine' contains: 1564
b'inferiortemporal' contains: 5501
b'middletemporal' contains: 5220
b'cuneus' contains: 2000
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[Freesurfer] Available postdoc position linked to ENIGMA Brain Injury

[Alexander Olsen]

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There is a temporary position available at the Department of Psychology as 
postdoctoral fellow in multimodal neuroimaging for a period of 2 years.The 
postdoctoral fellow will work at the Clinical Neuroscience Laboratory 
(CNL), headed by Associate professor 
Alexander Olsen.

The successful candidate will develop work that contributes to, and 
complements, ongoing research studies. The postdoctoral fellow will have a key 
role in our research activities linked to the ENIGMA Brain 
Injury working group. ENIGMA is 
a framework with harmonized protocols for data processing and analysis across 
multiple sites and cohorts. The postdoctoral fellow will work in close 
collaboration with our world-wide partners to provide new knowledge on the 
consequences of traumatic brain injury by utilizing an unprecedented sample 
size compared to typical neuroimaging studies. Salary starting at 515 200 NOK 
($ 62 000) per year.

Read more about the position, and how to apply: 
https://www.jobbnorge.no/ledige-stillinger/stilling/149964/postdoctoral-position-in-advanced-neuroimaging-at-the-clinical-neuroscience-laboratory-su-150

Feel free to contact me for any questions.

Sincerely,
Alexander Olsen
Associate Professor
Clinical Neuropsychologist
Norwegian University of Science and Technology
St. Olavs Hospital
Trondheim, Norway
Telephone: +47 917 22 824
http://www.ntnu.edu/employees/alexander.olsen







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[Freesurfer] freesurfer development version for mac incomplete

[Anik Dar]

External Email - Use Caution

Hi

When I try to download the development version of freesurfer for mac, the
file size is only 138 MB and doesnt unzip once downloaded.

Is there another link where the complete development version for mac can be
found ?

Thanks

Ani
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[Freesurfer] Seeing the Parcels as Volumes

[Maedeh Khalilian]

External Email - Use Caution

Dear FreeSurfer experts,
I have used "mri_annnotation2label" and "mri_label2vol" to change the 
parcellation output of FreeSurfer e.g the lh.aparc.annot into an ".nii" so i 
can see the parcels in Mricro.
Now I can see the parcels just on the cortex not on the whole graymatter.
The first question I have is that, is the parcellation done on the whole 
graymatter?
And if yes, is there a way that I can see the volumes on the whole 
graymatter, not just on the cortex?
I would be grateful if you could help me.
best regards,
Maedeh,___
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[Freesurfer] 3 positions to post on your platform

[Florence M]

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Hi,

Could you post this 3 positions on your forum please?

Best regards,
Florence Majri


biostatistican.docx
Description: MS-Word 2007 document


Research Engineer.docx
Description: MS-Word 2007 document


Postdoctoral Position on Imaging Genetics.docx
Description: MS-Word 2007 document
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