Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
Dear Bruce,
Many thanks for you answer!
I am trying to rerun the cortical reconstruction with the version 6.0 but I got the following error. May I have a license for this Freesurfer version 6.0?
Thanks a lot for your kind help!
Best regards,
Mohamed
-------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. --------------------------------------------------------------------------
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Mohamed,
You can download a new, free license for v6.0 directly from here: http://surfer.nmr.mgh.harvard.edu/registration.html
best, Andrew
On Jan 9, 2018, at 9:11 AM, m.bahri@uliege.bemailto:m.bahri@uliege.be wrote:
Dear Bruce,
Many thanks for you answer!
I am trying to rerun the cortical reconstruction with the version 6.0 but I got the following error. May I have a license for this Freesurfer version 6.0?
Thanks a lot for your kind help!
Best regards,
Mohamed
-------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/.license If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu/registration.html to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. --------------------------------------------------------------------------
----- Mail original ----- De: "Bruce Fischl" <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> À: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.bemailto:m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Université de Liège - University of Liège GIGA-Cyclotron Research Centre: In Vivo Imaging, Bât B30, Quartier Agora Allée du six Aout n°8 4000 Liège, Belgium m.bahri@uliege.be Tel : + 32-4-3662304
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce,
Attached is the screen shot of the results of the segmentation of the perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi does not cover the entire cortical thickness of the region. Is there any other alternative to get a better segmentation of this region?
Many thanks in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Mohamed
if you tar, gzip and ftp this subject to our ftp site we will take a look cheers Bruce On Thu, 18 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Attached is the screen shot of the results of the segmentation of the perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi does not cover the entire cortical thickness of the region. Is there any other alternative to get a better segmentation of this region?
Many thanks in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear Bruce,
Many thanks for your kind help!
I put the subject data on your ftp site (s8201.tar).
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Jeudi 18 Janvier 2018 16:37:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
if you tar, gzip and ftp this subject to our ftp site we will take a look cheers Bruce On Thu, 18 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Attached is the screen shot of the results of the segmentation of the perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi does not cover the entire cortical thickness of the region. Is there any other alternative to get a better segmentation of this region?
Many thanks in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Mohamed
how are you visualizing the MT or PC ROIs. Did you sample them into the volume? If so, can you tell me where the file ROIs are in the data you sent me?
cheers Bruce On Fri, 19 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Many thanks for your kind help!
I put the subject data on your ftp site (s8201.tar).
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Jeudi 18 Janvier 2018 16:37:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
if you tar, gzip and ftp this subject to our ftp site we will take a look cheers Bruce On Thu, 18 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Attached is the screen shot of the results of the segmentation of the perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi does not cover the entire cortical thickness of the region. Is there any other alternative to get a better segmentation of this region?
Many thanks in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear Bruce,
Thank you for your answer!
I just display the "T1.mgz" image (mri folder) using Freeview and then loaded the "lh/rh.perirhinal_exvivo.label" rois (label folder).
If this is not the good way to do it, please, could you explain more the procedure? What do you mean by MT and PC?
Thank you very much in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Vendredi 19 Janvier 2018 16:53:18 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
how are you visualizing the MT or PC ROIs. Did you sample them into the volume? If so, can you tell me where the file ROIs are in the data you sent me?
cheers Bruce On Fri, 19 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Many thanks for your kind help!
I put the subject data on your ftp site (s8201.tar).
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Jeudi 18 Janvier 2018 16:37:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
if you tar, gzip and ftp this subject to our ftp site we will take a look cheers Bruce On Thu, 18 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Attached is the screen shot of the results of the segmentation of the perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi does not cover the entire cortical thickness of the region. Is there any other alternative to get a better segmentation of this region?
Many thanks in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
oh, then I think you are just showing the surface-based label, which will only fill voxels that intersect with the white surface I believe. To sample it into the volume try mri_label2vol with the --fill-ribbon flag (the help is pretty extensive).
cheers Bruce On Mon, 22 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Thank you for your answer!
I just display the "T1.mgz" image (mri folder) using Freeview and then loaded the "lh/rh.perirhinal_exvivo.label" rois (label folder).
If this is not the good way to do it, please, could you explain more the procedure? What do you mean by MT and PC?
Thank you very much in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Vendredi 19 Janvier 2018 16:53:18 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
how are you visualizing the MT or PC ROIs. Did you sample them into the volume? If so, can you tell me where the file ROIs are in the data you sent me?
cheers Bruce On Fri, 19 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Many thanks for your kind help!
I put the subject data on your ftp site (s8201.tar).
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Jeudi 18 Janvier 2018 16:37:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
if you tar, gzip and ftp this subject to our ftp site we will take a look cheers Bruce On Thu, 18 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Attached is the screen shot of the results of the segmentation of the perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi does not cover the entire cortical thickness of the region. Is there any other alternative to get a better segmentation of this region?
Many thanks in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear Bruce,
Thank you very much for your kind help!
Best regards
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Lundi 22 Janvier 2018 16:12:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
oh, then I think you are just showing the surface-based label, which will only fill voxels that intersect with the white surface I believe. To sample it into the volume try mri_label2vol with the --fill-ribbon flag (the help is pretty extensive).
cheers Bruce On Mon, 22 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Thank you for your answer!
I just display the "T1.mgz" image (mri folder) using Freeview and then loaded the "lh/rh.perirhinal_exvivo.label" rois (label folder).
If this is not the good way to do it, please, could you explain more the procedure? What do you mean by MT and PC?
Thank you very much in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Vendredi 19 Janvier 2018 16:53:18 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
how are you visualizing the MT or PC ROIs. Did you sample them into the volume? If so, can you tell me where the file ROIs are in the data you sent me?
cheers Bruce On Fri, 19 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Many thanks for your kind help!
I put the subject data on your ftp site (s8201.tar).
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Jeudi 18 Janvier 2018 16:37:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
if you tar, gzip and ftp this subject to our ftp site we will take a look cheers Bruce On Thu, 18 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Attached is the screen shot of the results of the segmentation of the perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi does not cover the entire cortical thickness of the region. Is there any other alternative to get a better segmentation of this region?
Many thanks in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Dear Bruce,
Many thanks for you kind answer. I sampled the perirhinal roi label into the volume using the suggested command line: "mri_label2vol --subject s6904 --fill-ribbon --label lh.perirhinal.label --o lh.perirhinal.volume.nii --hemi lh --identity". The obtained mask seems to cover well the perirhinal structure.
Now, I calculate the perirhinal volmue (mm3) based on the obtained mask but I found that the obtained value does not match the one obtained during the Freesurfer cortical reconstruction (values in the stat folder: files : rh/lh-BA_exvivo.stats). did I messed something?
Thank you very much in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Lundi 22 Janvier 2018 16:12:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
oh, then I think you are just showing the surface-based label, which will only fill voxels that intersect with the white surface I believe. To sample it into the volume try mri_label2vol with the --fill-ribbon flag (the help is pretty extensive).
cheers Bruce On Mon, 22 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Thank you for your answer!
I just display the "T1.mgz" image (mri folder) using Freeview and then loaded the "lh/rh.perirhinal_exvivo.label" rois (label folder).
If this is not the good way to do it, please, could you explain more the procedure? What do you mean by MT and PC?
Thank you very much in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Vendredi 19 Janvier 2018 16:53:18 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
how are you visualizing the MT or PC ROIs. Did you sample them into the volume? If so, can you tell me where the file ROIs are in the data you sent me?
cheers Bruce On Fri, 19 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Many thanks for your kind help!
I put the subject data on your ftp site (s8201.tar).
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Jeudi 18 Janvier 2018 16:37:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
if you tar, gzip and ftp this subject to our ftp site we will take a look cheers Bruce On Thu, 18 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Attached is the screen shot of the results of the segmentation of the perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi does not cover the entire cortical thickness of the region. Is there any other alternative to get a better segmentation of this region?
Many thanks in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Mohamed
it depends on how you computed it. I believe that the one in the exvivo.stats file computes it directly from the surfaces (i.e. sum of the volumes of the tetrahedra or something like that). If you sample it into the volume and add up voxels you will get discretization artifacts that will change the volume.
cheers Bruce
On Thu, 8 Feb 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Many thanks for you kind answer. I sampled the perirhinal roi label into the volume using the suggested command line: "mri_label2vol --subject s6904 --fill-ribbon --label lh.perirhinal.label --o lh.perirhinal.volume.nii --hemi lh --identity". The obtained mask seems to cover well the perirhinal structure.
Now, I calculate the perirhinal volmue (mm3) based on the obtained mask but I found that the obtained value does not match the one obtained during the Freesurfer cortical reconstruction (values in the stat folder: files : rh/lh-BA_exvivo.stats). did I messed something?
Thank you very much in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Lundi 22 Janvier 2018 16:12:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
oh, then I think you are just showing the surface-based label, which will only fill voxels that intersect with the white surface I believe. To sample it into the volume try mri_label2vol with the --fill-ribbon flag (the help is pretty extensive).
cheers Bruce On Mon, 22 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Thank you for your answer!
I just display the "T1.mgz" image (mri folder) using Freeview and then loaded the "lh/rh.perirhinal_exvivo.label" rois (label folder).
If this is not the good way to do it, please, could you explain more the procedure? What do you mean by MT and PC?
Thank you very much in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Vendredi 19 Janvier 2018 16:53:18 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
how are you visualizing the MT or PC ROIs. Did you sample them into the volume? If so, can you tell me where the file ROIs are in the data you sent me?
cheers Bruce On Fri, 19 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Many thanks for your kind help!
I put the subject data on your ftp site (s8201.tar).
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Jeudi 18 Janvier 2018 16:37:10 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
if you tar, gzip and ftp this subject to our ftp site we will take a look cheers Bruce On Thu, 18 Jan 2018, m.bahri@uliege.be wrote:
Dear Bruce,
Attached is the screen shot of the results of the segmentation of the perirhinal Roi with Freesurfer V6. Unfortunately, as with V5 the segmented Roi does not cover the entire cortical thickness of the region. Is there any other alternative to get a better segmentation of this region?
Many thanks in advance,
Best regards,
Mohamed
----- Mail original ----- De: "Bruce Fischl" fischl@nmr.mgh.harvard.edu À: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Envoyé: Mardi 9 Janvier 2018 14:50:16 Objet: Re: [Freesurfer] freesurfer segmentation: perirhinal Roi
Hi Mohamed
I'm pretty sure this was an issue with the ribbon-filling in V5 that is better in V6. Try using it and see if it is fixed.
cheers Bruce On Tue, 9 Jan 2018, m.bahri@uliege.be wrote:
Dear Freesurfer experts,
We would like to use volume and cortical thickness measures obtained for the perirhinal cortex in Freesurfer 5. When checking the region that has been segmented (using lh/rh.perirhinal.label), we noticed that the ROI does not seem to cover the entire cortical thickness of the region. On the coronal slice shown in example (attached file), one can see that there are still a few voxels of gray matter between the external border of the ROI and the external boundary of the cortex. How reliable is this segmentation? Is there a reason why the ROI appears so thin?
Many thanks in advance,
Best regards,
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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