Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Ting Li]

External Email - Use Caution

The annot file loaded successfully and without any branches. Thanks a lot.

Ting
> On Oct 15, 2018, at 2:22 PM, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> Click on the surface file name in the upper left corner of FreeView, 
> then load the Annotation from the panel just below it. It does not make 
> sense that you would see the branches on the folded surface but not on 
> the inflated.
> 
> On 10/15/2018 03:06 PM, Ting Li wrote:
>> 
>> External Email - Use Caution
>> 
>> I didn't load the annot file. I just use the annot file to create the 
>> label. if I check the clusters in a inflated brain, they are looks 
>> fine. If I need to load annot file for checking, how can I do it? 
>> Thanks a lot.
>> 
>> Ting
>> 
>> On Mon, Oct 15, 2018 at 9:25 AM Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>> wrote:
>> 
>>does the same thing happen when you load the annot file?
>> 
>>On 10/13/18 10:03 PM, Ting Li wrote:
>>> 
>>>External Email - Use Caution
>>> 
>>>Dear Dr. Douglas,
>>> 
>>>I can load the label, but some clusters have branches. Some of
>>>them are just looks fine. Do you know the reason? Thanks a lot.
>>> 
>>>Regards,
>>>Ting
>>> 
>>> 
>>> 
>>> 
On Oct 12, 2018, at 10:35 AM, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
 
yes, that is fine
 
On 10/11/18 11:21 PM, Ting Li wrote:
> 
>External Email - Use Caution
> 
>Dear Dr. Douglas,
> 
>Thank you so much for your response. With your instruction, it
>works. This is how I did.
> 
>First, copy the significant cluster annot file from the
>simulation fold to one of subject label folder.
>Secondly, use the mir_annotation2label command to make this
>cluster into a label file
>Thirdly, copy this label file to fsaverage label folder
>Finally, I can load the label to the fsaverage surf.
> 
>Is this the right procedure? Thanks a lot!
> 
>Regards,
>Ting
>>On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D.
>>mailto:dgr...@mgh.harvard.edu>> wrote:
>> 
>>Which subject did you load it on? It must be fsaverage. Can
>>you send the
>>terminal output and command line?
>> 
>>On 10/03/2018 11:31 PM, Ting Li wrote:
>>> 
>>>External Email - Use Caution
>>> 
>>>Dear Freesurfer Expert,
>>> 
>>>I have figured out the problem is that I didn’t specify lh
>>>before the
>>>annot file. However, in this method, I didn’t get the right
>>>label for
>>>I have loaded the label into the subject file. It is the
>>>scatter points.
>>> 
>>>I want to create label through mri_glm-fit-sim clusters. What
>>>command
>>>I should use? Please specify it for me. Thanks a lot!
>>> 
>>>Your help means a lot.
>>> 
>>>Regards,
>>>Ting
On Oct 3, 2018, at 9:38 PM, Ting Li >>>
> wrote:
 
I have also tried the command without annot in specifying the
annotation file. Thanks a lot.
 
Regards,
 
Ting
>On Oct 3, 2018, at 9:36 PM, Ting Li 
>> wrote:
> 
>Dear Freesurfer Experts,
> 
>I really need your attention and help. Thanks a lot.
> 
>We want to create label through the mri_glm-fit-sim cluster
>results.
> 
>We have found the same topic in 2013 and tried the method
>you have
>provided. However, it doesn’t work. If you think it is not
>the right
>way, could you give me an example to do it right. I really
>appreciate your great help. Thanks a lot.
> 
>Here is my code:
> 
>mri_annotation2label --subject F999  --hemi lh --annotation
>cache.th20.neg.sig.ocn.annot --labelbase lh.test_label
> 
>Here is my error information:
>subject = F999
>annotation = cache.th20.neg.sig.ocn.annot
>hemi = lh
>labelbase = lh.test_label
>surface   = white
> 
>Reading surface
> /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white
>Loading annotations from
>
> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
>could not read annot file
>
> /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
>No such file or directory
>INFO: could not load from
>

[Freesurfer] Nonsensical Vertex Coordinates, please help with interpretation

[Bruss, Joel E]

External Email - Use Caution

I'm trying to make a surface file from a subject's head and to map coordinates 
to that surface.  If I run:


mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol 
$SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2 20 
--nhitsmin 2

mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255 
$SUBJECTS_DIR/$sub/surf/lh.seghead


and then load lh.seghead in FreeView, it looks as I would expect.  Clicking 
anywhere near a vertex gives the typical output, showing the closest vertex.  
All fine and well.  However, if I load the file in Matlab:


vCoord=read_surf('$SUBJECTS_DIR/$sub/surf/lh.seghead');


my values are nothing near what I'm seeing in Freeview.  For example, FreeView 
reports:


vertex 234741 [-78.50,14.50,26.50]


read_surf reports:


vertex 234740 0 168.9800 0

Of note, an error log tells me that:

MRISreadNewCurvature: incompatible vertex number in file 
$SUBJECTS_DIR/$sub/surf/lh.curv


How do I edit, update or create a curv file to play with the new surface file, 
or what can I do to get sensical surface coordinates from this data?

Thanks,
Joel









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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

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

Click on the surface file name in the upper left corner of FreeView, 
then load the Annotation from the panel just below it. It does not make 
sense that you would see the branches on the folded surface but not on 
the inflated.

On 10/15/2018 03:06 PM, Ting Li wrote:
>
> External Email - Use Caution
>
> I didn't load the annot file. I just use the annot file to create the 
> label. if I check the clusters in a inflated brain, they are looks 
> fine. If I need to load annot file for checking, how can I do it? 
> Thanks a lot.
>
> Ting
>
> On Mon, Oct 15, 2018 at 9:25 AM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> does the same thing happen when you load the annot file?
>
> On 10/13/18 10:03 PM, Ting Li wrote:
>>
>> External Email - Use Caution
>>
>> Dear Dr. Douglas,
>>
>> I can load the label, but some clusters have branches. Some of
>> them are just looks fine. Do you know the reason? Thanks a lot.
>>
>> Regards,
>> Ting
>>
>>
>>
>>
>>> On Oct 12, 2018, at 10:35 AM, Greve, Douglas N.,Ph.D.
>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>>
>>> yes, that is fine
>>>
>>> On 10/11/18 11:21 PM, Ting Li wrote:

 External Email - Use Caution

 Dear Dr. Douglas,

 Thank you so much for your response. With your instruction, it
 works. This is how I did.

 First, copy the significant cluster annot file from the
 simulation fold to one of subject label folder.
 Secondly, use the mir_annotation2label command to make this
 cluster into a label file
 Thirdly, copy this label file to fsaverage label folder
 Finally, I can load the label to the fsaverage surf.

 Is this the right procedure? Thanks a lot!

 Regards,
 Ting
> On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> Which subject did you load it on? It must be fsaverage. Can
> you send the
> terminal output and command line?
>
> On 10/03/2018 11:31 PM, Ting Li wrote:
>>
>> External Email - Use Caution
>>
>> Dear Freesurfer Expert,
>>
>> I have figured out the problem is that I didn’t specify lh
>> before the
>> annot file. However, in this method, I didn’t get the right
>> label for
>> I have loaded the label into the subject file. It is the
>> scatter points.
>>
>> I want to create label through mri_glm-fit-sim clusters. What
>> command
>> I should use? Please specify it for me. Thanks a lot!
>>
>> Your help means a lot.
>>
>> Regards,
>> Ting
>>> On Oct 3, 2018, at 9:38 PM, Ting Li >> 
>>> > wrote:
>>>
>>> I have also tried the command without annot in specifying the
>>> annotation file. Thanks a lot.
>>>
>>> Regards,
>>>
>>> Ting
 On Oct 3, 2018, at 9:36 PM, Ting Li >>> 
 > wrote:

 Dear Freesurfer Experts,

 I really need your attention and help. Thanks a lot.

 We want to create label through the mri_glm-fit-sim cluster
 results.

 We have found the same topic in 2013 and tried the method
 you have
 provided. However, it doesn’t work. If you think it is not
 the right
 way, could you give me an example to do it right. I really
 appreciate your great help. Thanks a lot.

 Here is my code:

 mri_annotation2label --subject F999  --hemi lh --annotation
 cache.th20.neg.sig.ocn.annot --labelbase lh.test_label

 Here is my error information:
 subject = F999
 annotation = cache.th20.neg.sig.ocn.annot
 hemi = lh
 labelbase = lh.test_label
 surface   = white

 Reading surface
  /media/set2iscsi/ting/origin_gz_data/F999/surf/lh.white
 Loading annotations from
 
 /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
 could not read annot file
 
 /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot
 No such file or directory
 INFO: could not load from
 
 /media/set2iscsi/ting/origin_gz_data/F999/label/lh.cache.th20.neg.sig.ocn.annot.annot,
 trying
 
 /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
 could not read annot file
 
 

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

[Bruce Fischl]

Hi Amanda

mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz

should do the trick
cheers
Bruce
On Mon, 15 Oct 
2018, Worker, Amanda wrote:




External Email - Use Caution

How would I do that? mris_convert doesn't seem to take .asc as an input?




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of
Greve, Douglas N.,Ph.D. 
Sent: 15 October 2018 16:25:51
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer  
Not sure. Can you use mris_convert to convert the asc back to a curv file?

On 10/15/2018 11:20 AM, Worker, Amanda wrote:
>
> External Email - Use Caution
>
> Hello,
>
>
> I am trying to overlay a .asc file in either freeview or tksurfer, but
> so far having no luck.
>
>
> As practice and to determine the right format, I am simply using
> lh.thickness, which I've converted to .asc using the following command:
>
>
> % mris_convert -c lh.thickness lh.white lh.thickness.asc
>
>
> I am trying to overlay this onto lh.pial for one subject, however I
> cannot load the file and I get the following error message:
>
>
> % mri_read(): couldn't determine type of file
>/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
ss.asc
> surfer: couldn't load
>/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
ss.asc.
>  If you were trying to load a functional volume, make sure
> you selected the right registration method, and if necessary,
> that the registration file exists.
> If you were trying to load a volume-encoded value file,
> make sure it has the same number of values as this surface
> does vertices (128970).
> sclv_read_from_volume: error in FunD_New
>
> Interestingly, I can load the file as a curvature file, but then can't
> play around with the threshold.
>
>
> Do you have any idea what I'm doing wrong? Any help would be appreciated!
>
>
> Thanks,
>
>
> Amanda
>
>
>
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Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

[Worker, Amanda]

External Email - Use Caution

How would I do that? mris_convert doesn't seem to take .asc as an input?




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

Sent: 15 October 2018 16:25:51
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

Not sure. Can you use mris_convert to convert the asc back to a curv file?

On 10/15/2018 11:20 AM, Worker, Amanda wrote:
>
> External Email - Use Caution
>
> Hello,
>
>
> I am trying to overlay a .asc file in either freeview or tksurfer, but
> so far having no luck.
>
>
> As practice and to determine the right format, I am simply using
> lh.thickness, which I've converted to .asc using the following command:
>
>
> % mris_convert -c lh.thickness lh.white lh.thickness.asc
>
>
> I am trying to overlay this onto lh.pial for one subject, however I
> cannot load the file and I get the following error message:
>
>
> % mri_read(): couldn't determine type of file
> /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc
> surfer: couldn't load
> /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc.
>  If you were trying to load a functional volume, make sure
> you selected the right registration method, and if necessary,
> that the registration file exists.
> If you were trying to load a volume-encoded value file,
> make sure it has the same number of values as this surface
> does vertices (128970).
> sclv_read_from_volume: error in FunD_New
>
> Interestingly, I can load the file as a curvature file, but then can't
> play around with the threshold.
>
>
> Do you have any idea what I'm doing wrong? Any help would be appreciated!
>
>
> Thanks,
>
>
> Amanda
>
>
>
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Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

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

Not sure. Can you use mris_convert to convert the asc back to a curv file?

On 10/15/2018 11:20 AM, Worker, Amanda wrote:
>
> External Email - Use Caution
>
> Hello,
>
>
> I am trying to overlay a .asc file in either freeview or tksurfer, but 
> so far having no luck.
>
>
> As practice and to determine the right format, I am simply using 
> lh.thickness, which I've converted to .asc using the following command:
>
>
> % mris_convert -c lh.thickness lh.white lh.thickness.asc
>
>
> I am trying to overlay this onto lh.pial for one subject, however I 
> cannot load the file and I get the following error message:
>
>
> % mri_read(): couldn't determine type of file 
> /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc
> surfer: couldn't load 
> /data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc.
>  If you were trying to load a functional volume, make sure
> you selected the right registration method, and if necessary,
> that the registration file exists.
> If you were trying to load a volume-encoded value file,
> make sure it has the same number of values as this surface
> does vertices (128970).
> sclv_read_from_volume: error in FunD_New
>
> Interestingly, I can load the file as a curvature file, but then can't 
> play around with the threshold.
>
>
> Do you have any idea what I'm doing wrong? Any help would be appreciated!
>
>
> Thanks,
>
>
> Amanda
>
>
>
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[Freesurfer] Using a .asc file as overlay in freeview/tksurfer

[Worker, Amanda]

External Email - Use Caution

Hello,


I am trying to overlay a .asc file in either freeview or tksurfer, but so far 
having no luck.


As practice and to determine the right format, I am simply using lh.thickness, 
which I've converted to .asc using the following command:


% mris_convert -c lh.thickness lh.white lh.thickness.asc


I am trying to overlay this onto lh.pial for one subject, however I cannot load 
the file and I get the following error message:


% mri_read(): couldn't determine type of file 
/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc
surfer: couldn't load 
/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickness.asc.
 If you were trying to load a functional volume, make sure
you selected the right registration method, and if necessary,
that the registration file exists.
If you were trying to load a volume-encoded value file,
make sure it has the same number of values as this surface
does vertices (128970).
sclv_read_from_volume: error in FunD_New

Interestingly, I can load the file as a curvature file, but then can't play 
around with the threshold.


Do you have any idea what I'm doing wrong? Any help would be appreciated!


Thanks,


Amanda
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Re: [Freesurfer] fMRI mask for hippocampal subfields

[Bruce Fischl]

Hi Chanelle

you can segment hippocampal subfields directly for individual subjects 
with the FreeSurfer tools written by Eugenio Iglesias:


https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

cheers
Bruce
On Mon, 15 
Oct 2018, 
Buckle, Chanelle [cbuc...@sun.ac.za] wrote:




External Email - Use Caution

Good day

 

I have fMRI data and would like to look at BOLD activation in the hippocampal 
subfields
(particularly the subiculum). I was wondering if there is currently an AAL mask 
available for the
hippocampal subfields or if there is some way to create it using the WFU 
Pickatlas Tool?

 

Kind regards,

Chanelle

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Re: [Freesurfer] qdec analysis with more than 2 covariates

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

You cannot use QDEC. For this case you'll need to use the "command line" 
stream. You'll need to start by creating an FSGD file
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples

On 10/15/18 10:15 AM, vittal korann wrote:

External Email - Use Caution

Hi Doug,

Recently I started working on freesurfer for volume based analysis. For QDEC, I 
need to include more than 2 variables. For example if I include patients who 
hail from different places like statutory town, census town and rural. In 
present scenario, can I include all three as covariates.
Here is the error that qdec showing while running GLM:

"ERROR: Subject 2 seems to have a mismatched number of discrete factors 
(expected 4, found 1)"
"Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
ERROR: no contrasts specified."
"Error in Analyze: command fai;ed mri_glmfit --y
/usr/local/freesurfer/subjects/qdec/qdecAnalys/y.mgh --fsgd
/usr/local/freesurfer/subjects/qdec/qdecAnalys/qdec.fsgd dods -glmdir
/usr/local/freesurfer/subjects/qdec/qdecAnalys/ -surf fsaverage lh -label
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label"

Could you help us out in this regard.

Would appreciate any help!!

Korann






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[Freesurfer] qdec analysis with more than 2 covariates

[vittal korann]

External Email - Use Caution

Hi Doug,

Recently I started working on freesurfer for volume based analysis. For
QDEC, I need to include more than 2 variables. For example if I include
patients who hail from different places like statutory town, census town
and rural. In present scenario, can I include all three as covariates.
Here is the error that qdec showing while running GLM:

"ERROR: Subject 2 seems to have a mismatched number of discrete factors
(expected 4, found 1)"
"Reading source surface
/usr/local/freesurfer/subjects/fsaverage/surf/lh.white
ERROR: no contrasts specified."
"Error in Analyze: command fai;ed mri_glmfit --y
/usr/local/freesurfer/subjects/qdec/qdecAnalys/y.mgh --fsgd
/usr/local/freesurfer/subjects/qdec/qdecAnalys/qdec.fsgd dods -glmdir
/usr/local/freesurfer/subjects/qdec/qdecAnalys/ -surf fsaverage lh -label
/usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label"

Could you help us out in this regard.

Would appreciate any help!!

Korann
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[Freesurfer] fMRI mask for hippocampal subfields

[Buckle, Chanelle [cbuc...@sun.ac.za]]

External Email - Use Caution

Good day

I have fMRI data and would like to look at BOLD activation in the hippocampal 
subfields (particularly the subiculum). I was wondering if there is currently 
an AAL mask available for the hippocampal subfields or if there is some way to 
create it using the WFU Pickatlas Tool?

Kind regards,
Chanelle
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