Re: [Freesurfer] Omitting aseg regions from segmentation

[Bruce Fischl]

Hi Kody

there definitely are flags like this in the dev version. e.g.:
case "-no-cerebellum":
case "-nocerebellum":
case "-NO-CEREBELLUM":
case "-NOCEREBELLUM":
set nocerebellum=( -nocerebellum)
breaksw ;

Maybe you should just grab the dev version?

And sorry, we haven't documented the ex vivo processing stream yet as it is 
too much of a work-in-progress.


cheers
Bruce


On Thu, 14 
Mar 2019, zalewk wrote:




External Email - Use Caution

Hi Bruce,

In response to your previous email, in v6.0 it doesn't look like recon-all has a 
"-no-cerebellum"
flag (or any cerebellum-related flags), I did verify that the recon-all script 
in the bin folder had
hemisphere-specific flags available however.

Is there any documentation on this? It still seems as if I'm missing something 
here, was it maybe
included in previous versions of freesurfer and removed?

Best,
Kody Zalewski

Date: Mon, 4 Mar 2019 15:07:26 -0500 (EST)
From: Bruce Fischl 
Subject: Re: [Freesurfer] Omitting aseg regions from segmentation
To: Freesurfer support list 
Message-ID:
    
Content-Type: text/plain; charset="iso-8859-1"

Hi Kody

yes, there are some hidden options to recon-all for this. Take a look at
the script for things like -no-cerebellum, -rh-only, and see if they are
sufficient for what you are trying to do

cheers
Bruce




On Mon, 4 Mar 2019, zalewk wrote:

>
> External Email - Use Caution
>
> Hello Freesurfer team,
>
> I am currently working processing the volumetrics of exvivo brains, many of 
which do not have a
> brainstem/cerebellum.
> It seems this often results in a subcortical alignment that isn't optimal, 
and fails to create the
> pial/wm surface where freesurfer attempts to label more ventral non-zero 
voxels as
> brainstem/cerebellum. Currently, I have to manually edit the
aseg.auto_noCCseg.label_intensities.mgz
> and aseg.presurf.mgz to fix this.
>
> Is there a way to omit aseg labels (like the brainstem/cerebellum) from the 
processing stream that
> I've overlooked? If not, would there be a potential alternate solution such 
as creating a second
> atlas from the original sans these ROIs and have the cross-sectional stream 
still run normally?
>
> Best,
> Kody Zalewski


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Re: [Freesurfer] Recon editing + FLAIRpial

[Bruce Fischl]

Hi Matthieu

Doug or Andrew can correct me if I'm wrong, but I believe you only need 
-FLAIR once (to import and normalize the flair volume), but you need to 
specify FLAIRpial each time if you want it to be rerun

cheers
Bruce


On Thu, 14 Mar 2019, Matthieu VANHOUTTE wrote:

>External Email - Use Caution
>
> Dear Experts,
>
> Having launched recon-all process on one subject with supplemental FLAIR
> data in order to better define pial surface, I still need to follow some
> recon editing during the QC of this patient.
>
> However, when re-launching recon-all to take into account manual editing
> do I have to precise on more time "-FLAIR FLAIR.nii.gz -FLAIRpial" or
> will it be implicit?
>
> Best regards,
>
> Matthieu
>
>
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>
>
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Re: [Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

[Martin Reuter]

Hi Arsenije, 

the file name should be  (with a starting “.” and no file extension): 

$SUBJECTS_DIR/qdec/.Qdecrc 

Best, Martin

> On 22. Feb 2019, at 00:22, Arsenije Subotic  
> wrote:
> 
> Dear Freesurfer experts,
> 
> I am having issues choosing the spc option for my QDEC two stage longitudinal 
> analysis as it is not there. The spc files are all present in my participants 
> files and the Qdecrc file is in the qdec subdirectory containing the line 
> long.thickness-spc. Is there a way to bypass this problem somehow?
> 
> Thank you,
> Arsenije
> 
> ---
> Arsenije Subotic | MSc Student 
> Department of Clinical Neurosciences
> Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada
> Tel: (403) 918-6970 
> arsenije.subot...@ucalgary.ca  
> 
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Re: [Freesurfer] Longitudinal QDEC

[Martin Reuter]

also note the file name starts with a “.”

.Qdecrc


> On 18. Mar 2019, at 21:16, Martin Reuter  wrote:
> 
> Hi Theo,
> 
> the file should be :
> $SUBJECTS_DIR/qdec/.Qdecrc
> 
> it is important that it is at that location and should not have an extension 
> (not .txt !)
> 
> Best, Martin
> 
>> On 18. Mar 2019, at 16:16, AKUDJEDU, THEOPHILUS > > wrote:
>> 
>> External Email - Use Caution
>> Dear All,
>> 
>> I am running a longitudinal (2-time points) group cortical analysis in 
>> Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
>> cross-sectional form, I added a text file containing the lines
>> MEASURE1 = long.thickness-avg
>> MEASURE2 = long.thickness-rate
>> MEASURE3 = long.thickness-pc1
>> MEASURE4 = long.thickness-spc
>> in the qdec directory to guide qdec to know about the newly created files 
>> (e.g. lh.long.thickness-spc...). However, it doesn't seem to be 
>> recognizing/picking up the new files or not reading the text file named 
>> Qdecrc.txt (which has the lines above. 
>> 
>> Will be glad if you could offer any help. 
>> 
>> Thanks 
>> 
>> Theo
>> 
>> 
>> 
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>> 

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Re: [Freesurfer] Longitudinal QDEC

[Martin Reuter]

Hi Theo,

the file should be :
$SUBJECTS_DIR/qdec/.Qdecrc

it is important that it is at that location and should not have an extension 
(not .txt !)

Best, Martin

> On 18. Mar 2019, at 16:16, AKUDJEDU, THEOPHILUS  
> wrote:
> 
> External Email - Use Caution
> Dear All,
> 
> I am running a longitudinal (2-time points) group cortical analysis in 
> Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
> cross-sectional form, I added a text file containing the lines
> MEASURE1 = long.thickness-avg
> MEASURE2 = long.thickness-rate
> MEASURE3 = long.thickness-pc1
> MEASURE4 = long.thickness-spc
> in the qdec directory to guide qdec to know about the newly created files 
> (e.g. lh.long.thickness-spc...). However, it doesn't seem to be 
> recognizing/picking up the new files or not reading the text file named 
> Qdecrc.txt (which has the lines above. 
> 
> Will be glad if you could offer any help. 
> 
> Thanks 
> 
> Theo
> 
> 
> 
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> 
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Re: [Freesurfer] tkregister-sess

[Nasiriavanaki, Zahra]

I changed my SUBJECTS_DIR folder, but I did not delete the old one at that time.




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

Sent: Monday, March 18, 2019 12:34:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tkregister-sess

Did you delete the bad registration file and re-run the registration 
(preproc-sess)?

On 3/18/19 11:53 AM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers


Hi

I was checking the functional on structural data registration quality by using  
the below command.

tkregister-sess -s $subj -fsd bold -per-run -bbr-sum

I observed high values (around 0.9) for one of my subjects, and I figured out, 
that subject was registered to another subject's structural data by mistake.

I re-did the recon (in a new folder) and checked the registration again, the 
values are still the same! However when I check my log files, it seems that the 
recon is done correctly and the snapshots from QA_tools don't look bad.

I appreciate if you could please let me know what you think.


Thanks a lot

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





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[Freesurfer] Time-series extraction from each vortex in a ROI

[Zhi Li]

External Email - Use Caution

Hello Freesurfer experts,

I would like to extract time series of pre-processed data from each vortex
of ROIs in a annotation file, may I ask how could I achieve this?  I tried
'mri_segstats' which only generated the mean time series of each ROI. I
also tried Matlab, but 'read_surf' doesn't seem to work in import brain
functional data (e.g., fmcpr.up.sm5.fsaverage.lh.nii.gz). If there is a way
to import functional data into Matlab? And how could I use the information
in the annotation file to get time series of each vortex in a ROI? Thank
you very much.

Best regards,

Lizhi
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Re: [Freesurfer] tkregister-sess

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

Did you delete the bad registration file and re-run the registration 
(preproc-sess)?

On 3/18/19 11:53 AM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers


Hi

I was checking the functional on structural data registration quality by using  
the below command.

tkregister-sess -s $subj -fsd bold -per-run -bbr-sum

I observed high values (around 0.9) for one of my subjects, and I figured out, 
that subject was registered to another subject's structural data by mistake.

I re-did the recon (in a new folder) and checked the registration again, the 
values are still the same! However when I check my log files, it seems that the 
recon is done correctly and the snapshots from QA_tools don't look bad.

I appreciate if you could please let me know what you think.


Thanks a lot

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129





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[Freesurfer] tkregister-sess

[Nasiriavanaki, Zahra]

Dear Freesurfers


Hi

I was checking the functional on structural data registration quality by using  
the below command.

tkregister-sess -s $subj -fsd bold -per-run -bbr-sum

I observed high values (around 0.9) for one of my subjects, and I figured out, 
that subject was registered to another subject's structural data by mistake.

I re-did the recon (in a new folder) and checked the registration again, the 
values are still the same! However when I check my log files, it seems that the 
recon is done correctly and the snapshots from QA_tools don't look bad.

I appreciate if you could please let me know what you think.


Thanks a lot

Mona


Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129


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[Freesurfer] skip subjects already processed

[Akshay Patel]

External Email - Use Caution

Hello,
I have a subset of subjects that were processed with an older version of
FreeSurfer and would like to run FreeSurfer in the subjects directory such
that it skips all the subjects already processed by my version of
freesurfer and only reruns recon-all ... for those aforementioned
subjects.

When I do this, will the file structure and files for the subject be
overwritten?  How does FreeSurfer behave in this case?  How does it behave
for subjects directories that have already been successfully processed with
the same command (including options) attempting to process it at the
moment?

Would appreciate any help thanks.

Best,
Akshay
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Re: [Freesurfer] Cortical thickness values extraction issue

[Giuliana Klencklen]

External Email - Use Caution

THank you so much for your help!

Le lun. 18 mars 2019 à 16:32, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :

> The vertices chosen for the cluster depend only on the cluster forming
> threshold (CFT). Once that is chosen, the vertices in the cluster are
> fixed. The permutation judges how likely the cluster as a whole would be
> seen by chance. There are other ways to do permutation, but this is the way
> we do it.
>
>
> On 3/18/19 11:25 AM, Giuliana Klencklen wrote:
>
> External Email - Use Caution
> Ok, well then I do not understand the purpose of the permutation testing
> if the number of permutation would not change the size of the clusters.
> What is it doing if not refining what vertices are significant? Perhaps I
> am just missing a key idea.
>
> Best,
>
>
> On Thu, Mar 14, 2019 at 5:11 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> The size of the cluster is not going to be affected by the number of
>> iterations (only by the threshold). Why would you think that the cluster
>> size is affected by the number of iterations?
>>
>> On 3/14/19 5:45 AM, Giuliana Klencklen wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hi Douglas,
>> >
>> > According to your suggestion, I used the permutation simulation
>> > approach. I chose a cluster forming threshold set at 0.05 and explored
>> > how the number of iterations effects the data. For example, I used
>> > this command for 1,000 iterations:
>> > mri_glmfit-sim \
>> >  --glmdir lh.longMRI.glmdir \
>> >  --sim perm 1000 1.3 perm.abs.13 \
>> >  --sim-sign abs\
>> >  --cwpvalthresh 0.05
>> >
>> > I did not observe any difference on the size of the cluster between
>> > 1,000 vs 5,000 vs 10,000 iterations. As I thought the results were
>> > pretty odd, I tried running the command with 5 permutations just to
>> > make sure it's not also the same and I did not find any significant
>> > clusters.
>> >
>> > Is the absence of cluster size difference between different number of
>> > iterations expected? Just wanted to make sure with you that this
>> > approach is working as it should.
>> >
>> > Thanks!
>> > Regards,
>> >
>> > On Fri, Feb 22, 2019 at 6:50 PM Greve, Douglas N.,Ph.D.
>> > mailto:dgr...@mgh.harvard.edu>> wrote:
>> >
>> > You can make the bonferroni correction from of mri_glmfit-sim the
>> > same as qdec by not including --2spaces (the bonferroni correction
>> > in qdec is actually 1, not 0). Also, if you want to use such a low
>> > cluster forming threshold (1.3=p<.05), then you should use
>> > permutation and not MC (MC is not valid at such low thresholds).
>> >
>> > On 2/22/19 7:49 AM, Giuliana Klencklen wrote:
>> >>
>> >> External Email - Use Caution
>> >>
>> >> Thanks Douglas, that makes sense. I have run mri_glmfit-sim and
>> >> have that table file.
>> >> However, the cortical thickness values for each cluster displayed
>> >> in that table can’t be used because the clusters
>> >> (something.sig.cluster.mgh opened with tksurfer) do not match
>> >> exactly (but are very similar to) those previously generated with
>> >> QDEC. I do not understand the cause of this issue because all the
>> >> stats I used, i.e., threshold, statistical correction, level of
>> >> smooting, seem to be the same between both qdec and mri_glmfit-sim.
>> >>
>> >> I send you here a typical example of the problematic clusters, as
>> >> well as the summary for both qdec and mri_glmfit-sim. They appear
>> >> similar except for the Bonferroni correction that is set at 2 for
>> >> the mri_glmfit-sim while it is set at 0 for the qdec version? If
>> >> it is the source of the current issue, how can I configure the
>> >> Bonferroni correction? If not, do you have any idea how I can
>> >> resolve the problem?
>> >>
>> >> Many thanks in advance.
>> >>
>> >> Regards,
>> >> Giuliana Klencklen
>> >> QdecGroupComparison.jpg
>> >>
>> >> On Fri, Feb 15, 2019 at 5:24 PM Greve, Douglas N.,Ph.D.
>> >> mailto:dgr...@mgh.harvard.edu>> wrote:
>> >>
>> >> This can happen if the label is small and/or you've used a
>> >> lot of smoothing. It is better to do this kind of thing in
>> >> fsaverage space rather than moving the labels back to the
>> >> individual space. If you've run mri_glmfit-sim, then it
>> >> should have created a table file  (something.y.ocn.dat). This
>> >> file will have a row for each subject and a column for each
>> >> cluster. The value will be the mean for that subject in that
>> >> cluster.
>> >>
>> >> On 2/15/19 6:23 AM, Giuliana Klencklen wrote:
>> >>>
>> >>> External Email - Use Caution
>> >>>
>> >>> Hi FS experts,
>> >>>
>> >>> I did group-level, surface-based, vertex-wise analysis for
>> >>> baseline and longitudinal data. I used Qdec and 

Re: [Freesurfer] Cortical thickness values extraction issue

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

The vertices chosen for the cluster depend only on the cluster forming 
threshold (CFT). Once that is chosen, the vertices in the cluster are fixed. 
The permutation judges how likely the cluster as a whole would be seen by 
chance. There are other ways to do permutation, but this is the way we do it.

On 3/18/19 11:25 AM, Giuliana Klencklen wrote:

External Email - Use Caution

Ok, well then I do not understand the purpose of the permutation testing if the 
number of permutation would not change the size of the clusters. What is it 
doing if not refining what vertices are significant? Perhaps I am just missing 
a key idea.

Best,


On Thu, Mar 14, 2019 at 5:11 PM Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
The size of the cluster is not going to be affected by the number of
iterations (only by the threshold). Why would you think that the cluster
size is affected by the number of iterations?

On 3/14/19 5:45 AM, Giuliana Klencklen wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> According to your suggestion, I used the permutation simulation
> approach. I chose a cluster forming threshold set at 0.05 and explored
> how the number of iterations effects the data. For example, I used
> this command for 1,000 iterations:
> mri_glmfit-sim \
>  --glmdir lh.longMRI.glmdir \
>  --sim perm 1000 1.3 perm.abs.13 \
>  --sim-sign abs\
>  --cwpvalthresh 0.05
>
> I did not observe any difference on the size of the cluster between
> 1,000 vs 5,000 vs 10,000 iterations. As I thought the results were
> pretty odd, I tried running the command with 5 permutations just to
> make sure it's not also the same and I did not find any significant
> clusters.
>
> Is the absence of cluster size difference between different number of
> iterations expected? Just wanted to make sure with you that this
> approach is working as it should.
>
> Thanks!
> Regards,
>
> On Fri, Feb 22, 2019 at 6:50 PM Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu> 
> >> wrote:
>
> You can make the bonferroni correction from of mri_glmfit-sim the
> same as qdec by not including --2spaces (the bonferroni correction
> in qdec is actually 1, not 0). Also, if you want to use such a low
> cluster forming threshold (1.3=p<.05), then you should use
> permutation and not MC (MC is not valid at such low thresholds).
>
> On 2/22/19 7:49 AM, Giuliana Klencklen wrote:
>>
>> External Email - Use Caution
>>
>> Thanks Douglas, that makes sense. I have run mri_glmfit-sim and
>> have that table file.
>> However, the cortical thickness values for each cluster displayed
>> in that table can’t be used because the clusters
>> (something.sig.cluster.mgh opened with tksurfer) do not match
>> exactly (but are very similar to) those previously generated with
>> QDEC. I do not understand the cause of this issue because all the
>> stats I used, i.e., threshold, statistical correction, level of
>> smooting, seem to be the same between both qdec and mri_glmfit-sim.
>>
>> I send you here a typical example of the problematic clusters, as
>> well as the summary for both qdec and mri_glmfit-sim. They appear
>> similar except for the Bonferroni correction that is set at 2 for
>> the mri_glmfit-sim while it is set at 0 for the qdec version? If
>> it is the source of the current issue, how can I configure the
>> Bonferroni correction? If not, do you have any idea how I can
>> resolve the problem?
>>
>> Many thanks in advance.
>>
>> Regards,
>> Giuliana Klencklen
>> QdecGroupComparison.jpg
>>
>> On Fri, Feb 15, 2019 at 5:24 PM Greve, Douglas N.,Ph.D.
>> mailto:dgr...@mgh.harvard.edu> 
>> >> wrote:
>>
>> This can happen if the label is small and/or you've used a
>> lot of smoothing. It is better to do this kind of thing in
>> fsaverage space rather than moving the labels back to the
>> individual space. If you've run mri_glmfit-sim, then it
>> should have created a table file  (something.y.ocn.dat). This
>> file will have a row for each subject and a column for each
>> cluster. The value will be the mean for that subject in that
>> cluster.
>>
>> On 2/15/19 6:23 AM, Giuliana Klencklen wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Hi FS experts,
>>>
>>> I did group-level, surface-based, vertex-wise analysis for
>>> baseline and longitudinal data. I used Qdec and do the same
>>> work with the fsgd version (mri_glmfit-sim command) to
>>> double-check the data.
>>>
>>> I created label files with tksurfer for each of the clusters
>>> showing a significant between-group difference. Then, I used
>>> the following command stream to extract the cortical

Re: [Freesurfer] Cortical thickness values extraction issue

[Giuliana Klencklen]

External Email - Use Caution

Ok, well then I do not understand the purpose of the permutation testing if
the number of permutation would not change the size of the clusters. What
is it doing if not refining what vertices are significant? Perhaps I am
just missing a key idea.

Best,


On Thu, Mar 14, 2019 at 5:11 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> The size of the cluster is not going to be affected by the number of
> iterations (only by the threshold). Why would you think that the cluster
> size is affected by the number of iterations?
>
> On 3/14/19 5:45 AM, Giuliana Klencklen wrote:
> >
> > External Email - Use Caution
> >
> > Hi Douglas,
> >
> > According to your suggestion, I used the permutation simulation
> > approach. I chose a cluster forming threshold set at 0.05 and explored
> > how the number of iterations effects the data. For example, I used
> > this command for 1,000 iterations:
> > mri_glmfit-sim \
> >  --glmdir lh.longMRI.glmdir \
> >  --sim perm 1000 1.3 perm.abs.13 \
> >  --sim-sign abs\
> >  --cwpvalthresh 0.05
> >
> > I did not observe any difference on the size of the cluster between
> > 1,000 vs 5,000 vs 10,000 iterations. As I thought the results were
> > pretty odd, I tried running the command with 5 permutations just to
> > make sure it's not also the same and I did not find any significant
> > clusters.
> >
> > Is the absence of cluster size difference between different number of
> > iterations expected? Just wanted to make sure with you that this
> > approach is working as it should.
> >
> > Thanks!
> > Regards,
> >
> > On Fri, Feb 22, 2019 at 6:50 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > You can make the bonferroni correction from of mri_glmfit-sim the
> > same as qdec by not including --2spaces (the bonferroni correction
> > in qdec is actually 1, not 0). Also, if you want to use such a low
> > cluster forming threshold (1.3=p<.05), then you should use
> > permutation and not MC (MC is not valid at such low thresholds).
> >
> > On 2/22/19 7:49 AM, Giuliana Klencklen wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Thanks Douglas, that makes sense. I have run mri_glmfit-sim and
> >> have that table file.
> >> However, the cortical thickness values for each cluster displayed
> >> in that table can’t be used because the clusters
> >> (something.sig.cluster.mgh opened with tksurfer) do not match
> >> exactly (but are very similar to) those previously generated with
> >> QDEC. I do not understand the cause of this issue because all the
> >> stats I used, i.e., threshold, statistical correction, level of
> >> smooting, seem to be the same between both qdec and mri_glmfit-sim.
> >>
> >> I send you here a typical example of the problematic clusters, as
> >> well as the summary for both qdec and mri_glmfit-sim. They appear
> >> similar except for the Bonferroni correction that is set at 2 for
> >> the mri_glmfit-sim while it is set at 0 for the qdec version? If
> >> it is the source of the current issue, how can I configure the
> >> Bonferroni correction? If not, do you have any idea how I can
> >> resolve the problem?
> >>
> >> Many thanks in advance.
> >>
> >> Regards,
> >> Giuliana Klencklen
> >> QdecGroupComparison.jpg
> >>
> >> On Fri, Feb 15, 2019 at 5:24 PM Greve, Douglas N.,Ph.D.
> >> mailto:dgr...@mgh.harvard.edu>> wrote:
> >>
> >> This can happen if the label is small and/or you've used a
> >> lot of smoothing. It is better to do this kind of thing in
> >> fsaverage space rather than moving the labels back to the
> >> individual space. If you've run mri_glmfit-sim, then it
> >> should have created a table file  (something.y.ocn.dat). This
> >> file will have a row for each subject and a column for each
> >> cluster. The value will be the mean for that subject in that
> >> cluster.
> >>
> >> On 2/15/19 6:23 AM, Giuliana Klencklen wrote:
> >>>
> >>> External Email - Use Caution
> >>>
> >>> Hi FS experts,
> >>>
> >>> I did group-level, surface-based, vertex-wise analysis for
> >>> baseline and longitudinal data. I used Qdec and do the same
> >>> work with the fsgd version (mri_glmfit-sim command) to
> >>> double-check the data.
> >>>
> >>> I created label files with tksurfer for each of the clusters
> >>> showing a significant between-group difference. Then, I used
> >>> the following command stream to extract the cortical
> >>> thickness values for each subject and cluster:
> >>> mri_label2label, mris_anatomical_stats, and aparcstats2table.
> >>> E.g.,
> >>> mri_label2label --srcsubject fsaverage --srclabel
> >>>
>  

Re: [Freesurfer] Longitudinal QDEC

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

Hi Theo, sorry, QDEC is not really being supported anymore. Try using the 
command line stream.

On 3/18/19 11:16 AM, AKUDJEDU, THEOPHILUS wrote:

External Email - Use Caution

Dear All,

I am running a longitudinal (2-time points) group cortical analysis in 
Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
cross-sectional form, I added a text file containing the lines

MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc

in the qdec directory to guide qdec to know about the newly created files (e.g. 
lh.long.thickness-spc...). However, it doesn't seem to be recognizing/picking 
up the new files or not reading the text file named Qdecrc.txt (which has the 
lines above.

Will be glad if you could offer any help.

Thanks

Theo






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Re: [Freesurfer] mris_preproc not running

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

can you send the terminal output? I realize it might be quite big. You can ftp 
it to here: /autofs/space/nihilus_001/CICS/ACRsoftware/ACRcurrent



On 3/18/19 11:12 AM, Sims, Sara A (Campus) wrote:

External Email - Use Caution
Hello!
I have 786 subjects that I am trying to do a paired difference analysis using 
mri_glm. I am getting stuck at the mris_preproc stage. I have tried running it 
on a handful of subjects and it works wonderfully. However, when I run it on 
all the subjects it outputs an empty file.
I think part of my problem is that I am having to do 1572 flags to enter all 
the subjects files (which I made a script to create, I did not hand type them). 
Is there a better way to do this? Do I just have too many subjects?

This is what I have that isn’t working:
mris_preproc --target fsaverage --hemi lh --isp 
$in/${network}/100206.${run1}/lhsurf.mgh --isp 
$in/${network}/100206.${run2}/lhsurf.mgh --isp 
$in/${network}/100307.${run1}/lhsurf.mgh --isp 
$in/${network}/100307.${run2}/lhsurf.mgh ……. --out 
$out/preproc_${network}_${pair}/lh.paired-diff.${network}_${pair}.mgh --f 
$sublist --paired-diff --no-cortex-only

Thanks for the help!

Sara Sims




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[Freesurfer] Longitudinal QDEC

[AKUDJEDU, THEOPHILUS]

External Email - Use Caution

Dear All,

I am running a longitudinal (2-time points) group cortical analysis in 
Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a 
cross-sectional form, I added a text file containing the lines

MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc

in the qdec directory to guide qdec to know about the newly created files (e.g. 
lh.long.thickness-spc...). However, it doesn't seem to be recognizing/picking 
up the new files or not reading the text file named Qdecrc.txt (which has the 
lines above.

Will be glad if you could offer any help.

Thanks

Theo



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[Freesurfer] mris_preproc not running

[Sims, Sara A (Campus)]

External Email - Use Caution

Hello!
I have 786 subjects that I am trying to do a paired difference analysis using 
mri_glm. I am getting stuck at the mris_preproc stage. I have tried running it 
on a handful of subjects and it works wonderfully. However, when I run it on 
all the subjects it outputs an empty file.
I think part of my problem is that I am having to do 1572 flags to enter all 
the subjects files (which I made a script to create, I did not hand type them). 
Is there a better way to do this? Do I just have too many subjects?

This is what I have that isn’t working:
mris_preproc --target fsaverage --hemi lh --isp 
$in/${network}/100206.${run1}/lhsurf.mgh --isp 
$in/${network}/100206.${run2}/lhsurf.mgh --isp 
$in/${network}/100307.${run1}/lhsurf.mgh --isp 
$in/${network}/100307.${run2}/lhsurf.mgh ……. --out 
$out/preproc_${network}_${pair}/lh.paired-diff.${network}_${pair}.mgh --f 
$sublist --paired-diff --no-cortex-only

Thanks for the help!

Sara Sims

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Re: [Freesurfer] Cortical Thickness Extraction

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

They do not have any normalization applied. BTW, you should not scale the 
thickness by the ICV

On 3/18/19 10:24 AM, Bunting, Emma wrote:

External Email - Use Caution
Hi Freesurfer experts,

I used a script created by ENIGMA to extract the cortical thickness values for 
129 subjects that had undergone reconall processing.


We are using these values in VBM analysis. From reading other papers, we notice 
that all regional volumes are usually normalised by dividing by total 
intracranial volumes for each subject.



I’m just wondering whether the values we are extracting from our freesurfer 
output files have already had this normalisation applied?

The script we’ve used as follows:


#!/bin/bash

echo 
'SubjID,L_bankssts_thickavg,L_caudalanteriorcingulate_thickavg,L_caudalmiddlefrontal_thickavg,L_cuneus_thickavg,L_entorhinal_thickavg,L_fusiform_thickavg,L_inferiorparietal_thickavg,L_inferiortemporal_thickavg,L_isthmuscingulate_thickavg,L_lateraloccipital_thickavg,L_lateralorbitofrontal_thickavg,L_lingual_thickavg,L_medialorbitofrontal_thickavg,L_middletemporal_thickavg,L_parahippocampal_thickavg,L_paracentral_thickavg,L_parsopercularis_thickavg,L_parsorbitalis_thickavg,L_parstriangularis_thickavg,L_pericalcarine_thickavg,L_postcentral_thickavg,L_posteriorcingulate_thickavg,L_precentral_thickavg,L_precuneus_thickavg,L_rostralanteriorcingulate_thickavg,L_rostralmiddlefrontal_thickavg,L_superiorfrontal_thickavg,L_superiorparietal_thickavg,L_superiortemporal_thickavg,L_supramarginal_thickavg,L_frontalpole_thickavg,L_temporalpole_thickavg,L_transversetemporal_thickavg,L_insula_thickavg,R_bankssts_thickavg,R_caudalanteriorcingulate_thickavg,R_caudalmiddlefrontal_thickavg,R_cuneus_thickavg,R_entorhinal_thickavg,R_fusiform_thickavg,R_inferiorparietal_thickavg,R_inferiortemporal_thickavg,R_isthmuscingulate_thickavg,R_lateraloccipital_thickavg,R_lateralorbitofrontal_thickavg,R_lingual_thickavg,R_medialorbitofrontal_thickavg,R_middletemporal_thickavg,R_parahippocampal_thickavg,R_paracentral_thickavg,R_parsopercularis_thickavg,R_parsorbitalis_thickavg,R_parstriangularis_thickavg,R_pericalcarine_thickavg,R_postcentral_thickavg,R_posteriorcingulate_thickavg,R_precentral_thickavg,R_precuneus_thickavg,R_rostralanteriorcingulate_thickavg,R_rostralmiddlefrontal_thickavg,R_superiorfrontal_thickavg,R_superiorparietal_thickavg,R_superiortemporal_thickavg,R_supramarginal_thickavg,R_frontalpole_thickavg,R_temporalpole_thickavg,R_transversetemporal_thickavg,R_insula_thickavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV'
 > CorticalMeasuresENIGMA_ThickAvg.csv
echo 
'SubjID,L_bankssts_surfavg,L_caudalanteriorcingulate_surfavg,L_caudalmiddlefrontal_surfavg,L_cuneus_surfavg,L_entorhinal_surfavg,L_fusiform_surfavg,L_inferiorparietal_surfavg,L_inferiortemporal_surfavg,L_isthmuscingulate_surfavg,L_lateraloccipital_surfavg,L_lateralorbitofrontal_surfavg,L_lingual_surfavg,L_medialorbitofrontal_surfavg,L_middletemporal_surfavg,L_parahippocampal_surfavg,L_paracentral_surfavg,L_parsopercularis_surfavg,L_parsorbitalis_surfavg,L_parstriangularis_surfavg,L_pericalcarine_surfavg,L_postcentral_surfavg,L_posteriorcingulate_surfavg,L_precentral_surfavg,L_precuneus_surfavg,L_rostralanteriorcingulate_surfavg,L_rostralmiddlefrontal_surfavg,L_superiorfrontal_surfavg,L_superiorparietal_surfavg,L_superiortemporal_surfavg,L_supramarginal_surfavg,L_frontalpole_surfavg,L_temporalpole_surfavg,L_transversetemporal_surfavg,L_insula_surfavg,R_bankssts_surfavg,R_caudalanteriorcingulate_surfavg,R_caudalmiddlefrontal_surfavg,R_cuneus_surfavg,R_entorhinal_surfavg,R_fusiform_surfavg,R_inferiorparietal_surfavg,R_inferiortemporal_surfavg,R_isthmuscingulate_surfavg,R_lateraloccipital_surfavg,R_lateralorbitofrontal_surfavg,R_lingual_surfavg,R_medialorbitofrontal_surfavg,R_middletemporal_surfavg,R_parahippocampal_surfavg,R_paracentral_surfavg,R_parsopercularis_surfavg,R_parsorbitalis_surfavg,R_parstriangularis_surfavg,R_pericalcarine_surfavg,R_postcentral_surfavg,R_posteriorcingulate_surfavg,R_precentral_surfavg,R_precuneus_surfavg,R_rostralanteriorcingulate_surfavg,R_rostralmiddlefrontal_surfavg,R_superiorfrontal_surfavg,R_superiorparietal_surfavg,R_superiortemporal_surfavg,R_supramarginal_surfavg,R_frontalpole_surfavg,R_temporalpole_surfavg,R_transversetemporal_surfavg,R_insula_surfavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV'
 > CorticalMeasuresENIGMA_SurfAvg.csv

for subj_id in $(ls -d Subj*); do #may need to change this so that it selects 
subjects with FS output

printf "%s,"  "${subj_id}" >> CorticalMeasuresENIGMA_ThickAvg.csv
printf "%s,"  "${subj_id}" >> CorticalMeasuresENIGMA_SurfAvg.csv

for side in lh.aparc.stats rh.aparc.stats; do

for x in bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal 
fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital 
lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal 
paracentral parsopercularis parsorbitalis parstriangularis pericalcarine 

Re: [Freesurfer] Video of brain inflating from the anatomy

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

See slide 30 here. does that work? If so, you have my permission to use it in 
your publication or presentation or whatever
http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.pptx

On 3/18/19 8:33 AM, Mageshwar Selvakumar wrote:

External Email - Use Caution

Dear Freesurfer Community,

We are working on a publication on chronic pain and for explanation purposes, 
we would like to show how the brain inflates from the anatomy. For this 
purpose, we thought a video on how inflation takes place could be interesting. 
I would like to know if there are some videos already made in this perspective 
and where it can be obtained. Looking forward to hearing from you.

Thank you,


Kind regards

Mageshwar Selvakumar, M.Sc

Department of Pharmakologische Bildgebung und Bildanalyse

Friedrich Alexander Universität Erlangen Nürnberg


Office: Fahrstr. 17, 91054 Erlangen

Phone: + 49-9131-8522898




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[Freesurfer] Cortical Thickness Extraction

[Bunting, Emma]

External Email - Use Caution

Hi Freesurfer experts,

I used a script created by ENIGMA to extract the cortical thickness values for 
129 subjects that had undergone reconall processing.


We are using these values in VBM analysis. From reading other papers, we notice 
that all regional volumes are usually normalised by dividing by total 
intracranial volumes for each subject.



I’m just wondering whether the values we are extracting from our freesurfer 
output files have already had this normalisation applied?

The script we’ve used as follows:


#!/bin/bash

echo 
'SubjID,L_bankssts_thickavg,L_caudalanteriorcingulate_thickavg,L_caudalmiddlefrontal_thickavg,L_cuneus_thickavg,L_entorhinal_thickavg,L_fusiform_thickavg,L_inferiorparietal_thickavg,L_inferiortemporal_thickavg,L_isthmuscingulate_thickavg,L_lateraloccipital_thickavg,L_lateralorbitofrontal_thickavg,L_lingual_thickavg,L_medialorbitofrontal_thickavg,L_middletemporal_thickavg,L_parahippocampal_thickavg,L_paracentral_thickavg,L_parsopercularis_thickavg,L_parsorbitalis_thickavg,L_parstriangularis_thickavg,L_pericalcarine_thickavg,L_postcentral_thickavg,L_posteriorcingulate_thickavg,L_precentral_thickavg,L_precuneus_thickavg,L_rostralanteriorcingulate_thickavg,L_rostralmiddlefrontal_thickavg,L_superiorfrontal_thickavg,L_superiorparietal_thickavg,L_superiortemporal_thickavg,L_supramarginal_thickavg,L_frontalpole_thickavg,L_temporalpole_thickavg,L_transversetemporal_thickavg,L_insula_thickavg,R_bankssts_thickavg,R_caudalanteriorcingulate_thickavg,R_caudalmiddlefrontal_thickavg,R_cuneus_thickavg,R_entorhinal_thickavg,R_fusiform_thickavg,R_inferiorparietal_thickavg,R_inferiortemporal_thickavg,R_isthmuscingulate_thickavg,R_lateraloccipital_thickavg,R_lateralorbitofrontal_thickavg,R_lingual_thickavg,R_medialorbitofrontal_thickavg,R_middletemporal_thickavg,R_parahippocampal_thickavg,R_paracentral_thickavg,R_parsopercularis_thickavg,R_parsorbitalis_thickavg,R_parstriangularis_thickavg,R_pericalcarine_thickavg,R_postcentral_thickavg,R_posteriorcingulate_thickavg,R_precentral_thickavg,R_precuneus_thickavg,R_rostralanteriorcingulate_thickavg,R_rostralmiddlefrontal_thickavg,R_superiorfrontal_thickavg,R_superiorparietal_thickavg,R_superiortemporal_thickavg,R_supramarginal_thickavg,R_frontalpole_thickavg,R_temporalpole_thickavg,R_transversetemporal_thickavg,R_insula_thickavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV'
 > CorticalMeasuresENIGMA_ThickAvg.csv
echo 
'SubjID,L_bankssts_surfavg,L_caudalanteriorcingulate_surfavg,L_caudalmiddlefrontal_surfavg,L_cuneus_surfavg,L_entorhinal_surfavg,L_fusiform_surfavg,L_inferiorparietal_surfavg,L_inferiortemporal_surfavg,L_isthmuscingulate_surfavg,L_lateraloccipital_surfavg,L_lateralorbitofrontal_surfavg,L_lingual_surfavg,L_medialorbitofrontal_surfavg,L_middletemporal_surfavg,L_parahippocampal_surfavg,L_paracentral_surfavg,L_parsopercularis_surfavg,L_parsorbitalis_surfavg,L_parstriangularis_surfavg,L_pericalcarine_surfavg,L_postcentral_surfavg,L_posteriorcingulate_surfavg,L_precentral_surfavg,L_precuneus_surfavg,L_rostralanteriorcingulate_surfavg,L_rostralmiddlefrontal_surfavg,L_superiorfrontal_surfavg,L_superiorparietal_surfavg,L_superiortemporal_surfavg,L_supramarginal_surfavg,L_frontalpole_surfavg,L_temporalpole_surfavg,L_transversetemporal_surfavg,L_insula_surfavg,R_bankssts_surfavg,R_caudalanteriorcingulate_surfavg,R_caudalmiddlefrontal_surfavg,R_cuneus_surfavg,R_entorhinal_surfavg,R_fusiform_surfavg,R_inferiorparietal_surfavg,R_inferiortemporal_surfavg,R_isthmuscingulate_surfavg,R_lateraloccipital_surfavg,R_lateralorbitofrontal_surfavg,R_lingual_surfavg,R_medialorbitofrontal_surfavg,R_middletemporal_surfavg,R_parahippocampal_surfavg,R_paracentral_surfavg,R_parsopercularis_surfavg,R_parsorbitalis_surfavg,R_parstriangularis_surfavg,R_pericalcarine_surfavg,R_postcentral_surfavg,R_posteriorcingulate_surfavg,R_precentral_surfavg,R_precuneus_surfavg,R_rostralanteriorcingulate_surfavg,R_rostralmiddlefrontal_surfavg,R_superiorfrontal_surfavg,R_superiorparietal_surfavg,R_superiortemporal_surfavg,R_supramarginal_surfavg,R_frontalpole_surfavg,R_temporalpole_surfavg,R_transversetemporal_surfavg,R_insula_surfavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV'
 > CorticalMeasuresENIGMA_SurfAvg.csv

for subj_id in $(ls -d Subj*); do #may need to change this so that it selects 
subjects with FS output

printf "%s,"  "${subj_id}" >> CorticalMeasuresENIGMA_ThickAvg.csv
printf "%s,"  "${subj_id}" >> CorticalMeasuresENIGMA_SurfAvg.csv

for side in lh.aparc.stats rh.aparc.stats; do

for x in bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal 
fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital 
lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal 
paracentral parsopercularis parsorbitalis parstriangularis pericalcarine 
postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate 
rostralmiddlefrontal superiorfrontal superiorparietal 

[Freesurfer] Video of brain inflating from the anatomy

[Mageshwar Selvakumar]

External Email - Use Caution

Dear Freesurfer Community,

We are working on a publication on chronic pain and for explanation purposes, 
we would like to show how the brain inflates from the anatomy. For this 
purpose, we thought a video on how inflation takes place could be interesting. 
I would like to know if there are some videos already made in this perspective 
and where it can be obtained. Looking forward to hearing from you.

Thank you,


Kind regards

Mageshwar Selvakumar, M.Sc

Department of Pharmakologische Bildgebung und Bildanalyse

Friedrich Alexander Universität Erlangen Nürnberg


Office: Fahrstr. 17, 91054 Erlangen

Phone: + 49-9131-8522898

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