subject:"Re\: \[Freesurfer\] create label from cluster obtained with mri

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

2018-10-16 Thread Ting Li

External Email - Use Caution

If I loaded the label to the inflated surface, it also gives me the cluster 
with branches. As you can see in the below. 

If I loaded the annot file to the inflated surface, it works well. Thanks for 
your help. 

Ting 



> On Oct 16, 2018, at 1:51 PM, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> Hmm, not sure what to tell you. The label is derived directly from the 
> annot. If you click on a vertex in the branch, does it appear to be in 
> the label based on what displays in the control panel? If you load it on 
> the inflated surface, do you still see the branch?
> 
> On 10/15/2018 08:42 PM, Ting Li wrote:
>> 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:
>>> 
>

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

2018-10-16 Thread Greve, Douglas N.,Ph.D.

Hmm, not sure what to tell you. The label is derived directly from the 
annot. If you click on a vertex in the branch, does it appear to be in 
the label based on what displays in the control panel? If you load it on 
the inflated surface, do you still see the branch?

On 10/15/2018 08:42 PM, Ting Li wrote:
>  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
>>  /

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

2018-10-15 Thread 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
>
>>

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

2018-10-15 Thread 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
 
 /media/set2iscs

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

2018-10-12 Thread Greve, Douglas N.,Ph.D.

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 mailto:tx...@ualr.edu>
> 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 mailto:tx...@ualr.edu>
> 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
/media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
No such file or directory
ERROR: MRISreadAnnotation() failed

This is the annot files in my directory F999:
ls F999/label/*.annot
F999/label/cache.th20.neg.sig.ocn.annot
F999/label/lh.BA_exvivo.annot F999/label/rh.aparc.DKTatlas.annot
F999/label/lh.aparc.a2009s.annot
F999/label/lh.BA_exvivo.thresh.annot F999/label/rh.BA_exvivo.annot
F999/label/lh.aparc.annot F999/label/rh.aparc.a2009s.annot
F999/label/rh.BA_exvivo.thresh.annot
F999/label/lh.aparc.DKTatlas.annot   F999/label/rh.aparc.annot

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

2018-10-11 Thread Ting Li

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.  
> 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 
 /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
 No such file or directory
 ERROR: MRISreadAnnotation() failed
 
 This is the annot files in my directory F999:
 ls F999/label/*.annot
 F999/label/cache.th20.neg.sig.ocn.annot 
 F999/label/lh.BA_exvivo.annot F999/label/rh.aparc.DKTatlas.annot
 F999/label/lh.aparc.a2009s.annot 
 F999/label/lh.BA_exvivo.thresh.annot F999/label/rh.BA_exvivo.annot
 F999/label/lh.aparc.annot F999/label/rh.aparc.a2009s.annot 
 F999/label/rh.BA_exvivo.thresh.annot
 F999/label/lh.aparc.DKTatlas.annot   F999/label/rh.aparc.annot
>>> 
>> 
>> 
>> 
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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

2018-10-10 Thread Greve, Douglas N.,Ph.D.

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 
>>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
>>> No such file or directory
>>> ERROR: MRISreadAnnotation() failed
>>>
>>> This is the annot files in my directory F999:
>>> ls F999/label/*.annot
>>> F999/label/cache.th20.neg.sig.ocn.annot 
>>> F999/label/lh.BA_exvivo.annot F999/label/rh.aparc.DKTatlas.annot
>>> F999/label/lh.aparc.a2009s.annot 
>>> F999/label/lh.BA_exvivo.thresh.annot F999/label/rh.BA_exvivo.annot
>>> F999/label/lh.aparc.annot F999/label/rh.aparc.a2009s.annot 
>>> F999/label/rh.BA_exvivo.thresh.annot
>>> F999/label/lh.aparc.DKTatlas.annot       F999/label/rh.aparc.annot
>>
>
>
>
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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

2018-10-03 Thread Ting Li

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 mailto:tx...@ualr.edu>> 
>> 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 
>> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
>> No such file or directory
>> ERROR: MRISreadAnnotation() failed
>> 
>> This is the annot files in my directory F999:
>> ls F999/label/*.annot
>> F999/label/cache.th20.neg.sig.ocn.annot  F999/label/lh.BA_exvivo.annot   
>>   F999/label/rh.aparc.DKTatlas.annot
>> F999/label/lh.aparc.a2009s.annot 
>> F999/label/lh.BA_exvivo.thresh.annot  F999/label/rh.BA_exvivo.annot
>> F999/label/lh.aparc.annotF999/label/rh.aparc.a2009s.annot
>>   F999/label/rh.BA_exvivo.thresh.annot
>> F999/label/lh.aparc.DKTatlas.annot   F999/label/rh.aparc.annot
> 

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

2018-10-03 Thread Ting Li

External Email - Use Caution

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 
> /media/set2iscsi/ting/origin_gz_data/F999/label/lh_cache.th20.neg.sig.ocn.annot.annot
> No such file or directory
> ERROR: MRISreadAnnotation() failed
> 
> This is the annot files in my directory F999:
> ls F999/label/*.annot
> F999/label/cache.th20.neg.sig.ocn.annot  F999/label/lh.BA_exvivo.annot
>  F999/label/rh.aparc.DKTatlas.annot
> F999/label/lh.aparc.a2009s.annot F999/label/lh.BA_exvivo.thresh.annot 
>  F999/label/rh.BA_exvivo.annot
> F999/label/lh.aparc.annotF999/label/rh.aparc.a2009s.annot 
>  F999/label/rh.BA_exvivo.thresh.annot
> F999/label/lh.aparc.DKTatlas.annot   F999/label/rh.aparc.annot

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

2013-08-15 Thread Garikoitz Lerma-Usabiaga

Sorry Doug,
I don't understand, I just have the cluster.mgh file with the MonteCarlo
simulation results, is an .mgh file with a big significant cluster (
mc-z.abs.sig.cluster.mgh).

Is there a way to create a label for each of the significant clusters?

thanks again and sorry if the question is too trivial!
Gari




On Thu, Aug 15, 2013 at 7:32 PM, Douglas N Greve
wrote:

> Give it the annotation (.annot) file
>
>
>
>
>
> On 08/15/2013 01:26 PM, Garikoitz Lerma-Usabiaga wrote:
>
>> Thanks Doug!
>> Could you give me an example please?  I cannot get it to work, with this
>> command I get a zero label...
>>
>> mri_annotation2label --subject fsaverage --hemi lh --annotation
>> lh.mc-z.abs.sig.cluster.mgh --labelbase lh.mc_mycluster
>>
>> thanks again!
>> Gari
>>
>>
>>
>> On Thu, Aug 15, 2013 at 4:44 PM, Douglas Greve 
>> > gr...@nmr.mgh.harvard.**edu >> wrote:
>>
>>
>> Hi Gari, you can use mri_annotation2label
>> doug
>>
>>
>> On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote:
>>
>>> Hi list,
>>> we have a cluster that survived the Monte Carlo simulation for
>>> thickness, and we would like to obtain more data from that exact
>>> cluster (volume for example), is it possible to automatically
>>> create a label from that cluster?
>>>
>>> If I use mri_binarize or mri_cor2label is not working (I
>>> understand that the clusters are not stored as individual
>>> vertexes in the .mgh file but I don't know what the format is.
>>>
>>> Thanks in advance!
>>> Gari
>>>
>>> PD: I am on a VPN and tksurfer is not working for manually
>>> creating a label with the contour of the cluster.
>>>
>>>
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>>
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>>
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> --
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> greve/ 
>
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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

2013-08-15 Thread Garikoitz Lerma-Usabiaga

Thanks Doug!
Could you give me an example please?  I cannot get it to work, with this
command I get a zero label...

mri_annotation2label --subject fsaverage --hemi lh --annotation
lh.mc-z.abs.sig.cluster.mgh --labelbase lh.mc_mycluster

thanks again!
Gari



On Thu, Aug 15, 2013 at 4:44 PM, Douglas Greve wrote:

>
> Hi Gari, you can use mri_annotation2label
> doug
>
>
> On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote:
>
> Hi list,
> we have a cluster that survived the Monte Carlo simulation for thickness,
> and we would like to obtain more data from that exact cluster (volume for
> example), is it possible to automatically create a label from that cluster?
>
>  If I use mri_binarize or mri_cor2label is not working (I understand that
> the clusters are not stored as individual vertexes in the .mgh file but I
> don't know what the format is.
>
>  Thanks in advance!
> Gari
>
>  PD: I am on a VPN and tksurfer is not working for manually creating a
> label with the contour of the cluster.
>
>
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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

2013-08-15 Thread Douglas Greve



Hi Gari, you can use mri_annotation2label
doug

On 8/14/13 3:00 PM, Garikoitz Lerma-Usabiaga wrote:

Hi list,
we have a cluster that survived the Monte Carlo simulation for 
thickness, and we would like to obtain more data from that exact 
cluster (volume for example), is it possible to automatically create a 
label from that cluster?


If I use mri_binarize or mri_cor2label is not working (I understand 
that the clusters are not stored as individual vertexes in the .mgh 
file but I don't know what the format is.


Thanks in advance!
Gari

PD: I am on a VPN and tksurfer is not working for manually creating a 
label with the contour of the cluster.



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

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

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

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

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

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

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

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

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

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

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

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

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