create label from cluster obtained with mri_glm-fit-sim

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Ting Li

3 Oct 2018 3 Oct '18

10:36 p.m.

External Email - Use Caution

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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Ting Li

3 Oct 3 Oct

10:38 p.m.

New subject: create label from cluster obtained with mri_glm-fit-sim

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 txli1@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

Ting Li

11:31 p.m.

New subject: create label from cluster obtained with mri_glm-fit-sim

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 txli1@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 <txli1@ualr.edu mailto:txli1@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

Greve, Douglas N.,Ph.D.

10 Oct 10 Oct

2:30 p.m.

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 <txli1@ualr.edu mailto:txli1@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 <txli1@ualr.edu mailto:txli1@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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Ting Li

11 Oct 11 Oct

11:21 p.m.

New subject: create label from cluster obtained with mri_glm-fit-sim

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. DGREVE@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 <txli1@ualr.edu <mailto:txli1@ualr.edu mailto:txli1@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 <txli1@ualr.edu mailto:txli1@ualr.edu <mailto:txli1@ualr.edu mailto:txli1@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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Greve, Douglas N.,Ph.D.

12 Oct 12 Oct

11:35 a.m.

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.

Is this the right procedure? Thanks a lot!

Regards, Ting On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@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 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 <txli1@ualr.edumailto:txli1@ualr.edu mailto:txli1@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 <txli1@ualr.edumailto:txli1@ualr.edu mailto:txli1@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.

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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Ting Li

13 Oct 13 Oct

10:03 p.m.

New subject: create label from cluster obtained with mri_glm-fit-sim

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. DGREVE@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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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 <txli1@ualr.edu mailto:txli1@ualr.edu <mailto:txli1@ualr.edu mailto:txli1@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 <txli1@ualr.edu mailto:txli1@ualr.edu <mailto:txli1@ualr.edu mailto:txli1@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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Greve, Douglas N.,Ph.D.

15 Oct 15 Oct

10:24 a.m.

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

[cid:part1.46D71C82.5FF0D177@mgh.harvard.edu]

[cid:part2.865F64D6.F15D5CF0@mgh.harvard.edu] On Oct 12, 2018, at 10:35 AM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@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.

Is this the right procedure? Thanks a lot!

Regards, Ting On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@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 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 <txli1@ualr.edumailto:txli1@ualr.edu mailto:txli1@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 <txli1@ualr.edumailto:txli1@ualr.edu mailto:txli1@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.

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

Ting Li

3:06 p.m.

New subject: create label from cluster obtained with mri_glm-fit-sim

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. < DGREVE@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. < DGREVE@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. < DGREVE@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 <txli1@ualr.edu <mailto:txli1@ualr.edu txli1@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 <txli1@ualr.edu <mailto:txli1@ualr.edu txli1@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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Greve, Douglas N.,Ph.D.

3:22 p.m.

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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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.
<DGREVE@mgh.harvard.edu <mailto:DGREVE@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.
<DGREVE@mgh.harvard.edu <mailto:DGREVE@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 <txli1@ualr.edu > mailto:txli1@ualr.edu > mailto:txli1@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 <txli1@ualr.edu >> mailto:txli1@ualr.edu >> mailto:txli1@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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Ting Li

8:42 p.m.

New subject: create label from cluster obtained with mri_glm-fit-sim

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. DGREVE@mgh.harvard.edu 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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 <txli1@ualr.edu >> mailto:txli1@ualr.edu >> mailto:txli1@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 <txli1@ualr.edu >>> mailto:txli1@ualr.edu >>> mailto:txli1@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 >> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Greve, Douglas N.,Ph.D.

16 Oct 16 Oct

2:51 p.m.

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. DGREVE@mgh.harvard.edu 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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.
<DGREVE@mgh.harvard.edu <mailto:DGREVE@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. > <DGREVE@mgh.harvard.edu mailto:DGREVE@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 <txli1@ualr.edu >>> mailto:txli1@ualr.edu >>> mailto:txli1@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 <txli1@ualr.edu >>>> mailto:txli1@ualr.edu >>>> mailto:txli1@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 >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Ting Li

10:29 p.m.

New subject: create label from cluster obtained with mri_glm-fit-sim

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. DGREVE@mgh.harvard.edu 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:

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

Ting

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On Oct 15, 2018, at 2:22 PM, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu 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:

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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. <DGREVE@mgh.harvard.edu mailto:DGREVE@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:

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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

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On Oct 12, 2018, at 10:35 AM, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@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. >> <DGREVE@mgh.harvard.edu mailto:DGREVE@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 <txli1@ualr.edu >>>> mailto:txli1@ualr.edu >>>> mailto:txli1@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 <txli1@ualr.edu >>>>> mailto:txli1@ualr.edu >>>>> mailto:txli1@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 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> mailto:Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Greve, Douglas N.,Ph.D.
Ting Li