Re: [Freesurfer] Problem with cortical parcellation of rh but not lh
Hi Bruce, I sent you two subject's directories through FileDrop. Thanks! Cheers Amal From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Wednesday, February 21, 2018 6:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] Problem with cortical parcellation of rh but not lh Hi Amal we need the entire directory tree for that subject cheers Bruce On Wed, 21 Feb 2018, Amal Achaibou wrote: > > Hi, > > Yes I've seen it for multiple subjects. > > I'm using version 6. > > Here are the results for one participants, let me know if you need any other > file. > > Thanks > > > Amal > > > > > > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of > Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Sent: Thursday, February 15, 2018 8:37 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Problem with cortical parcellation of rh but not lh > Hi Amal > > this happens for multiple subjects? What version are you using? I have > only ever seen this very rarely and usually for an atypical (e.g. > multiple central sulci) folding pattern. Can you upload a subject so I > can take a look? > > cheers > Bruce > On Tue, 13 Feb 2018, Amal Achaibou wrote: > > > > > Hello, > > > > I'm new to freesurfer and have been trying to use it for cortical > > parcellation of individual T1s > > running recon-all -s subID -i sunT1 -all command. I'm specifically > > interested in getting > > parahippocampal and perirhinal ROIs for each individual. It appears that > > the parcellation is > correct > > for the left hemisphere but not for the right hemisphere... I found that > > there were also > mislabeling > > for precentral and postcentral gyrus (as easy gyri to identify), and that > > regardless of if I > looked > > at the aparc.annot or the aparc.DKTatlas.annot parcellation scheme. > > > > Is there any reason why I have this systematic mistake? Attached is the > > example for one subject > > (others looked very similar). > > > > > > Thanks > > > > > > Amal > > > > > >___ > _ > > > > > > > ___ > 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.
Re: [Freesurfer] Problem with cortical parcellation of rh but not lh
Hi Amal we need the entire directory tree for that subject cheers Bruce On Wed, 21 Feb 2018, Amal Achaibou wrote: Hi, Yes I've seen it for multiple subjects. I'm using version 6. Here are the results for one participants, let me know if you need any other file. Thanks Amal From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Thursday, February 15, 2018 8:37 PM To: Freesurfer support list Subject: Re: [Freesurfer] Problem with cortical parcellation of rh but not lh Hi Amal this happens for multiple subjects? What version are you using? I have only ever seen this very rarely and usually for an atypical (e.g. multiple central sulci) folding pattern. Can you upload a subject so I can take a look? cheers Bruce On Tue, 13 Feb 2018, Amal Achaibou wrote: > > Hello, > > I'm new to freesurfer and have been trying to use it for cortical parcellation of individual T1s > running recon-all -s subID -i sunT1 -all command. I'm specifically interested in getting > parahippocampal and perirhinal ROIs for each individual. It appears that the parcellation is correct > for the left hemisphere but not for the right hemisphere... I found that there were also mislabeling > for precentral and postcentral gyrus (as easy gyri to identify), and that regardless of if I looked > at the aparc.annot or the aparc.DKTatlas.annot parcellation scheme. > > Is there any reason why I have this systematic mistake? Attached is the example for one subject > (others looked very similar). > > > Thanks > > > Amal > > >___ _ > > > ___ 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.
Re: [Freesurfer] Problem with cortical parcellation of rh but not lh
Hi Amal this happens for multiple subjects? What version are you using? I have only ever seen this very rarely and usually for an atypical (e.g. multiple central sulci) folding pattern. Can you upload a subject so I can take a look? cheers Bruce On Tue, 13 Feb 2018, Amal Achaibou wrote: > > Hello, > > I'm new to freesurfer and have been trying to use it for cortical > parcellation of individual T1s > running recon-all -s subID -i sunT1 -all command. I'm specifically interested > in getting > parahippocampal and perirhinal ROIs for each individual. It appears that the > parcellation is correct > for the left hemisphere but not for the right hemisphere... I found that > there were also mislabeling > for precentral and postcentral gyrus (as easy gyri to identify), and that > regardless of if I looked > at the aparc.annot or the aparc.DKTatlas.annot parcellation scheme. > > Is there any reason why I have this systematic mistake? Attached is the > example for one subject > (others looked very similar). > > > Thanks > > > Amal > > > > > > ___ 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.
Re: [Freesurfer] Problem with the parcellation
Wan, I've started looking into this for you. We've recently built a version of freesurfer under Tiger, and I've run parcellate_subject and mris_anatomical_stats, and I am also seeing the problem you are seeing where 'annotate' is displayed in the output instead of the proper names. I'll see what I can find. It's a strange problem. Nick On Mon, 2005-06-13 at 10:21 -0300, Wan Park wrote: __ Hello, I have been running freesurfer in G5 Macs with Panther. I was able to parcellate and retrieve data of the different areas. However, recently we changed the OS from Panther to Tiger. Since then, I have the following problem: When I do mris_anatomical_stats: [ogden:freesurfer_package/freesurfer/subjects] wpark% mris_anatomical_stats -b -a 14649/label/rh.aparc.annot 14649 rh computing statistics for each annotation in 14649/label/rh.aparc.annot. reading volume /usr/local/freesurfer_package/freesurfer/subjects/14649/mri/wm... reading input surface /usr/local/freesurfer_package/freesurfer/subjects/14649/surf/rh.white... INFO: Volume /tmp/mritotal_2576/orig_8_dxyz.mnc cannot be found. INFO: found the orig volume (mri/orig) to get c_(ras) information for src INFO: added info to the surface. done. computing second fundamental form...reading colortable from annotation file... colortable with 0 entries read (originally ) done. total white matter volume = 509402 mm^3 table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard error (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 3758 2149 4165 1.950 +- 0.579 0.199 0.067 75.676 9.502 ** annotation 003c148c 2251 1174 3233 2.652 +- 0.702 0.200 0.081 67.771 6.118 ** annotation 00b43cb4 1285731 1674 2.284 +- 0.590 0.179 0.065 25.068 2.573 ** annotation 003cdc14 1282792 1629 2.076 +- 0.523 0.170 0.041 14.336 1.902 ** annotation 00dc3c65 1304794 1569 2.005 +- 0.501 0.190 0.044 19.070 2.299 ** annotation 008c1415 306137291 2.137 +- 0.534 0.147 0.0253.083 0.471 ** annotation 00b43c15 1604935 1722 1.840 +- 0.477 0.203 0.070 34.702 3.964 ** annotation 001414b4 2363 1479 3196 2.165 +- 0.602 0.160 0.035 27.198 3.101 ** annotation 00b46465 2602 1659 3292 1.968 +- 0.729 0.189 0.052 47.088 5.998 ** annotation 00b4b43f 2299 1339 3348 2.510 +- 0.575 0.192 0.051 50.159 4.279 ** annotation 00dcb4dc 548309766 2.469 +- 0.454 0.165 0.0435.623 0.997 ** annotation 00c8c80a 1015591 1455 2.481 +- 0.499 0.196 0.056 24.732 1.704 ** annotation 0064dc8c .. Instead of having the name of different areas, I receive annotation... Curiously, this does not happen if I do mris_anatomical_stats in previously parcellated brains (before the new installation). This happens when I parcellate_subject and then I try to get the info of the areas. This is what I got when I parcellate: [ogden:freesurfer_package/freesurfer/subjects] wpark% parcellate_subject 14649 reading atlas from /usr/local/freesurfer_package/freesurfer/average/lh.atlas2002_simple.gcs... reading color table from GCSA file reading color table from GCSA file input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 9935 changed, 137093 examined... 001: 2397 changed, 37088 examined... 002:731 changed, 1 examined... 003:340 changed, 4117 examined... 004:155 changed, 1818 examined... 005: 88 changed, 871 examined... 006: 47 changed, 459 examined... 007: 28 changed, 255 examined... 008: 19 changed, 160 examined... 009: 12 changed, 97 examined... 010: 10 changed, 64 examined... 011: 5 changed, 64 examined... 012: 3 changed, 27 examined... 013: 2 changed, 19 examined... 014: 1 changed, 9 examined... 015: 0 changed, 6 examined... 000: 340 total segments, 238 labels (3015 vertices) changed 001: 123 total segments, 23 labels (316 vertices) changed 002: 104 total segments, 4 labels (20 vertices) changed 003: 100 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 164 changed) writing output to /usr/local/freesurfer_package/freesurfer/subjects/14649/label/lh.aparc.annot... writing colortable into annotation file... classification took 3 minutes and 42 seconds. reading atlas from /usr/local/freesurfer_package/freesurfer/average/rh.atlas2002_simple.gcs... reading color table from GCSA file reading
[Freesurfer] Problem with the parcellation
Hello, I have been running freesurfer in G5 Macs with Panther. I was able to parcellate and retrieve data of the different areas. However, recently we changed the OS from Panther to Tiger. Since then, I have the following problem: When I do mris_anatomical_stats: [ogden:freesurfer_package/freesurfer/subjects] wpark% mris_anatomical_stats -b -a 14649/label/rh.aparc.annot 14649 rh computing statistics for each annotation in 14649/label/rh.aparc.annot. reading volume /usr/local/freesurfer_package/freesurfer/subjects/14649/mri/wm... reading input surface /usr/local/freesurfer_package/freesurfer/subjects/14649/surf/rh.white... INFO: Volume /tmp/mritotal_2576/orig_8_dxyz.mnc cannot be found. INFO: found the orig volume (mri/orig) to get c_(ras) information for src INFO: added info to the surface. done. computing second fundamental form...reading colortable from annotation file... colortable with 0 entries read (originally ) done. total white matter volume = 509402 mm^3 table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard error (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 3758 2149 4165 1.950 +- 0.579 0.199 0.067 75.676 9.502 ** annotation 003c148c 2251 1174 3233 2.652 +- 0.702 0.200 0.081 67.771 6.118 ** annotation 00b43cb4 1285731 1674 2.284 +- 0.590 0.179 0.065 25.068 2.573 ** annotation 003cdc14 1282792 1629 2.076 +- 0.523 0.170 0.041 14.336 1.902 ** annotation 00dc3c65 1304794 1569 2.005 +- 0.501 0.190 0.044 19.070 2.299 ** annotation 008c1415 306137291 2.137 +- 0.534 0.147 0.0253.083 0.471 ** annotation 00b43c15 1604935 1722 1.840 +- 0.477 0.203 0.070 34.702 3.964 ** annotation 001414b4 2363 1479 3196 2.165 +- 0.602 0.160 0.035 27.198 3.101 ** annotation 00b46465 2602 1659 3292 1.968 +- 0.729 0.189 0.052 47.088 5.998 ** annotation 00b4b43f 2299 1339 3348 2.510 +- 0.575 0.192 0.051 50.159 4.279 ** annotation 00dcb4dc 548309766 2.469 +- 0.454 0.165 0.0435.623 0.997 ** annotation 00c8c80a 1015591 1455 2.481 +- 0.499 0.196 0.056 24.732 1.704 ** annotation 0064dc8c .. Instead of having the name of different areas, I receive annotation... Curiously, this does not happen if I do mris_anatomical_stats in previously parcellated brains (before the new installation). This happens when I parcellate_subject and then I try to get the info of the areas. This is what I got when I parcellate: [ogden:freesurfer_package/freesurfer/subjects] wpark% parcellate_subject 14649 reading atlas from /usr/local/freesurfer_package/freesurfer/average/lh.atlas2002_simple.gcs... reading color table from GCSA file reading color table from GCSA file input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 9935 changed, 137093 examined... 001: 2397 changed, 37088 examined... 002:731 changed, 1 examined... 003:340 changed, 4117 examined... 004:155 changed, 1818 examined... 005: 88 changed, 871 examined... 006: 47 changed, 459 examined... 007: 28 changed, 255 examined... 008: 19 changed, 160 examined... 009: 12 changed, 97 examined... 010: 10 changed, 64 examined... 011: 5 changed, 64 examined... 012: 3 changed, 27 examined... 013: 2 changed, 19 examined... 014: 1 changed, 9 examined... 015: 0 changed, 6 examined... 000: 340 total segments, 238 labels (3015 vertices) changed 001: 123 total segments, 23 labels (316 vertices) changed 002: 104 total segments, 4 labels (20 vertices) changed 003: 100 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 164 changed) writing output to /usr/local/freesurfer_package/freesurfer/subjects/14649/label/lh.aparc.annot... writing colortable into annotation file... classification took 3 minutes and 42 seconds. reading atlas from /usr/local/freesurfer_package/freesurfer/average/rh.atlas2002_simple.gcs... reading color table from GCSA file reading color table from GCSA file input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 9869 changed, 137521 examined... 001: 2399 changed, 36932 examined... 002:698 changed, 12235 examined... 003:282 changed, 3952 examined... 004:150 changed, 1565 examined... 005: 81 changed, 821 examined... 006: 58 changed, 453 examined... 007: 30 changed, 299 examined... 008: 10 changed, 170 examined... 009: 4 changed, 54 examined... 010: 4 changed, 26 examined...
