External Email - Use Caution

Thanks, it works. Does the code mean that it only allows labels under 300 to pass through?

Best, Qi

On Fri, Jun 5, 2020 at 12:37 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Dear Qi,

You can try:

mri_threshold -U [lr]h.hippoAmygLabels-T1.v21.mgz 300 [lr]h.hippoLabelsNoAmyg-T1.v21.mgz

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Zeng, Qi" < qi.zeng@icahn.mssm.edu> *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, June 5, 2020 at 11:54 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

•    External Email - Use Caution        *
  
  

Hi,

I conducted longitudinal segmentation of both hippocampus and amygdala from running segmentHA_T1_long.sh. But is it possible for me to segment only the hippocampus region "mgz" from the stored [lr]h.hippoAmygLabels-T1.long.v21.mgz ?

Best,

Qi

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

---

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

External Email - Use Caution

Thanks. I was wondering If there is another way around to get the amygdala mgz.

Best, Qi

On Fri, Jun 5, 2020 at 2:44 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Yes 😊 the amydala labels are in the 7000 range and the hippocampal in the 200s. Feel free to use eg 4129 next time!

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Zeng, Qi" < qi.zeng@icahn.mssm.edu> *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, June 5, 2020 at 14:42 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

•    External Email - Use Caution        *
  
  

Thanks, it works. Does the code mean that it only allows labels under 300 to pass through?

Best,

Qi

On Fri, Jun 5, 2020 at 12:37 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Dear Qi,

You can try:

mri_threshold -U [lr]h.hippoAmygLabels-T1.v21.mgz 300 [lr]h.hippoLabelsNoAmyg-T1.v21.mgz

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Zeng, Qi" < qi.zeng@icahn.mssm.edu> *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, June 5, 2020 at 11:54 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

•    External Email - Use Caution        *
  
  

Hi,

I conducted longitudinal segmentation of both hippocampus and amygdala from running segmentHA_T1_long.sh. But is it possible for me to segment only the hippocampus region "mgz" from the stored [lr]h.hippoAmygLabels-T1.long.v21.mgz ?

Best,

Qi

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

---

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

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

---

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

External Email - Use Caution

Hi Juan,

If I want to seed T1 hippocampus.mgz to fill the ProbtrackX. How should I do that? Is it something like below: mris_convert lh.white lh.white.gii mri_convert lh.hippocampus.mgz lh.hippocampus.nii.gz and then label2surf -s lh.white.gii -o lh.hippocampus.nii.gz -l hippocampus.txt

Thank you so much !

Best, Qi

On Fri, Jun 5, 2020 at 4:13 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Removing the -U ;-)

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Zeng, Qi" < qi.zeng@icahn.mssm.edu> *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, June 5, 2020 at 16:02 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

•    External Email - Use Caution        *
  
  

Thanks. I was wondering If there is another way around to get the amygdala mgz.

Best,

Qi

On Fri, Jun 5, 2020 at 2:44 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Yes 😊 the amydala labels are in the 7000 range and the hippocampal in the 200s. Feel free to use eg 4129 next time!

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Zeng, Qi" < qi.zeng@icahn.mssm.edu> *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, June 5, 2020 at 14:42 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

•    External Email - Use Caution        *
  
  

Thanks, it works. Does the code mean that it only allows labels under 300 to pass through?

Best,

Qi

On Fri, Jun 5, 2020 at 12:37 PM Iglesias Gonzalez, Juan E. < JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Dear Qi,

You can try:

mri_threshold -U [lr]h.hippoAmygLabels-T1.v21.mgz 300 [lr]h.hippoLabelsNoAmyg-T1.v21.mgz

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Zeng, Qi" < qi.zeng@icahn.mssm.edu> *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, June 5, 2020 at 11:54 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Get hippocampus segmention from [lr]h.hippoAmygLabels-T1.v21.mgz

•    External Email - Use Caution        *
  
  

Hi,

I conducted longitudinal segmentation of both hippocampus and amygdala from running segmentHA_T1_long.sh. But is it possible for me to segment only the hippocampus region "mgz" from the stored [lr]h.hippoAmygLabels-T1.long.v21.mgz ?

Best,

Qi

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

---

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

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

---

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

--

Ph.D. candidate

Icahn School of Medicine at Mount Sinai

---

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