Re: [Freesurfer] recon-all on newborn
Thanks Emma for sharing the link. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Boyd, Emma [ebo...@mgh.harvard.edu] Sent: 07 July 2017 15:51 To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn Hi Sarbani, Please see this paper for more information: https://www.ncbi.nlm.nih.gov/pubmed/25741260 Emma From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Das S. <sarbani@soton.ac.uk> Sent: Friday, July 7, 2017 4:58:39 AM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn Is there any paper that you can share that can explain why recon-all is not suitable for neonates brain apart from atlas. Sarbani -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lilla Zollei Sent: 06 July 2017 21:43 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all on newborn It is not only the atlas but the tools that are different. Lilla On Wed, 5 Jul 2017, Das S. wrote: > Dear Lilla, > In that case you mean if I have my own atlas specific to neonates then I can > follow these steps of auto recon. > If you give me little more details will be easy for me to understand the gap. > many thanks > Sarbani > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei > [lzol...@nmr.mgh.harvard.edu] > Sent: 05 July 2017 22:32 > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all on newborn > > We use a similar pipeline but with different atlases and processing > steps for the newborns. > Lilla > > On Wed, 5 Jul 2017, Das S. wrote: > >> >> Thanks for the reply. If you let me know, among the below list of steps of >> current recon-all, currently which is not suitable to perform on neonates >> MRI image, will really appreciate. >> >> Autorecon Processing Stages: >>Motion Correction and Conform >>NU (Non-Uniform intensity normalization) >>Talairach transform computation >>Intensity Normalization 1 >>Skull Strip >>EM Register (linear volumetric registration) >>CA Intensity Normalization >>CA Non-linear Volumetric Registration >>Remove Neck >>LTA with Skull >>CA Label (Volumetric Labeling, ie Aseg) and Statistics >>Intensity Normalization 2 (start here for control points) >>White matter segmentation >>Edit WM With ASeg >>Fill (start here for wm edits) >>Tessellation (begins per-hemisphere operations) >>Smooth1 >>Inflate1 >>QSphere >>Automatic Topology Fixer >>Final Surfs (start here for brain edits for pial surf) >>Smooth2 >>Inflate2 >>Spherical Mapping >>Spherical Registration >>Spherical Registration, Contralateral hemisphere >>Map average curvature to subject >>Cortical Parcellation - Desikan_Killiany and Christophe (Labeling) >>Cortical Parcellation Statistics >>Cortical Ribbon Mask >>Cortical Parcellation mapping to Aseg >> >> BW >> S Das >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei >> [lzol...@nmr.mgh.harvard.edu] >> Sent: 04 July 2017 22:04 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all on newborn >> >> Hi S Das, >> >> We are trying to release the infant pipeline by the end of the summer. >> >> Lilla >> >> On Tue, 4 Jul 2017, Das S. wrote: >> >>> Dear Freesurfer expert, >>> I want to perform recon-all pipeline on neonates data.Can I do so? >>> I was going through some mail archives and there it is said that on T1 >>> image of neonates data we can't perform recon-all. >>> But again there is another paper where it says Freesurfer can perform >>> segmentation of neonates image. >>> Any input will be appreciated. >>> Thanks >>> S Das >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.
Re: [Freesurfer] recon-all on newborn
Thanks for your reply.Much appreciated. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 07 July 2017 15:06 To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn because neonate geometry and lack of myelin cause the brains to look so different from what many of our algorithms expect. cheers Bruce On Fri, 7 Jul 2017, Das S. wrote: > Is there any paper that you can share that can explain why recon-all is not > suitable for neonates brain apart from atlas. > Sarbani > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lilla Zollei > Sent: 06 July 2017 21:43 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] recon-all on newborn > > > It is not only the atlas but the tools that are different. > > Lilla > > On Wed, 5 Jul 2017, Das S. wrote: > >> Dear Lilla, >> In that case you mean if I have my own atlas specific to neonates then I can >> follow these steps of auto recon. >> If you give me little more details will be easy for me to understand the gap. >> many thanks >> Sarbani >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei >> [lzol...@nmr.mgh.harvard.edu] >> Sent: 05 July 2017 22:32 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all on newborn >> >> We use a similar pipeline but with different atlases and processing >> steps for the newborns. >> Lilla >> >> On Wed, 5 Jul 2017, Das S. wrote: >> >>> >>> Thanks for the reply. If you let me know, among the below list of steps of >>> current recon-all, currently which is not suitable to perform on neonates >>> MRI image, will really appreciate. >>> >>> Autorecon Processing Stages: >>>Motion Correction and Conform >>>NU (Non-Uniform intensity normalization) >>>Talairach transform computation >>>Intensity Normalization 1 >>>Skull Strip >>>EM Register (linear volumetric registration) >>>CA Intensity Normalization >>>CA Non-linear Volumetric Registration >>>Remove Neck >>>LTA with Skull >>>CA Label (Volumetric Labeling, ie Aseg) and Statistics >>>Intensity Normalization 2 (start here for control points) >>>White matter segmentation >>>Edit WM With ASeg >>>Fill (start here for wm edits) >>>Tessellation (begins per-hemisphere operations) >>>Smooth1 >>>Inflate1 >>>QSphere >>>Automatic Topology Fixer >>>Final Surfs (start here for brain edits for pial surf) >>>Smooth2 >>>Inflate2 >>>Spherical Mapping >>>Spherical Registration >>>Spherical Registration, Contralateral hemisphere >>>Map average curvature to subject >>>Cortical Parcellation - Desikan_Killiany and Christophe (Labeling) >>>Cortical Parcellation Statistics >>>Cortical Ribbon Mask >>> Cortical Parcellation mapping to Aseg >>> >>> BW >>> S Das >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei >>> [lzol...@nmr.mgh.harvard.edu] >>> Sent: 04 July 2017 22:04 >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] recon-all on newborn >>> >>> Hi S Das, >>> >>> We are trying to release the infant pipeline by the end of the summer. >>> >>> Lilla >>> >>> On Tue, 4 Jul 2017, Das S. wrote: >>> >>>> Dear Freesurfer expert, >>>> I want to perform recon-all pipeline on neonates data.Can I do so? >>>> I was going through some mail archives and there it is said that on T1 >>>> image of neonates data we can't perform recon-all. >>>> But again there is another paper where it says Freesurfer can perform >>>> segmentation of neonates image. >>>> Any input will be appreciated. >>>> Thanks >>>> S Das >>>> >>>> >>>> ___ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.ed
Re: [Freesurfer] recon-all on newborn
Is there any paper that you can share that can explain why recon-all is not suitable for neonates brain apart from atlas. Sarbani -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lilla Zollei Sent: 06 July 2017 21:43 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] recon-all on newborn It is not only the atlas but the tools that are different. Lilla On Wed, 5 Jul 2017, Das S. wrote: > Dear Lilla, > In that case you mean if I have my own atlas specific to neonates then I can > follow these steps of auto recon. > If you give me little more details will be easy for me to understand the gap. > many thanks > Sarbani > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei > [lzol...@nmr.mgh.harvard.edu] > Sent: 05 July 2017 22:32 > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all on newborn > > We use a similar pipeline but with different atlases and processing > steps for the newborns. > Lilla > > On Wed, 5 Jul 2017, Das S. wrote: > >> >> Thanks for the reply. If you let me know, among the below list of steps of >> current recon-all, currently which is not suitable to perform on neonates >> MRI image, will really appreciate. >> >> Autorecon Processing Stages: >>Motion Correction and Conform >>NU (Non-Uniform intensity normalization) >>Talairach transform computation >>Intensity Normalization 1 >>Skull Strip >>EM Register (linear volumetric registration) >>CA Intensity Normalization >>CA Non-linear Volumetric Registration >>Remove Neck >>LTA with Skull >>CA Label (Volumetric Labeling, ie Aseg) and Statistics >>Intensity Normalization 2 (start here for control points) >>White matter segmentation >>Edit WM With ASeg >>Fill (start here for wm edits) >>Tessellation (begins per-hemisphere operations) >>Smooth1 >>Inflate1 >>QSphere >>Automatic Topology Fixer >>Final Surfs (start here for brain edits for pial surf) >>Smooth2 >>Inflate2 >>Spherical Mapping >>Spherical Registration >>Spherical Registration, Contralateral hemisphere >>Map average curvature to subject >>Cortical Parcellation - Desikan_Killiany and Christophe (Labeling) >>Cortical Parcellation Statistics >>Cortical Ribbon Mask >>Cortical Parcellation mapping to Aseg >> >> BW >> S Das >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei >> [lzol...@nmr.mgh.harvard.edu] >> Sent: 04 July 2017 22:04 >> To: Freesurfer support list >> Subject: Re: [Freesurfer] recon-all on newborn >> >> Hi S Das, >> >> We are trying to release the infant pipeline by the end of the summer. >> >> Lilla >> >> On Tue, 4 Jul 2017, Das S. wrote: >> >>> Dear Freesurfer expert, >>> I want to perform recon-all pipeline on neonates data.Can I do so? >>> I was going through some mail archives and there it is said that on T1 >>> image of neonates data we can't perform recon-all. >>> But again there is another paper where it says Freesurfer can perform >>> segmentation of neonates image. >>> Any input will be appreciated. >>> Thanks >>> S Das >>> >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> ___ >> 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 >> Freesur
Re: [Freesurfer] recon-all on newborn
Dear Lilla, In that case you mean if I have my own atlas specific to neonates then I can follow these steps of auto recon. If you give me little more details will be easy for me to understand the gap. many thanks Sarbani From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzol...@nmr.mgh.harvard.edu] Sent: 05 July 2017 22:32 To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn We use a similar pipeline but with different atlases and processing steps for the newborns. Lilla On Wed, 5 Jul 2017, Das S. wrote: > > Thanks for the reply. If you let me know, among the below list of steps of > current recon-all, currently which is not suitable to perform on neonates MRI > image, will really appreciate. > > Autorecon Processing Stages: >Motion Correction and Conform >NU (Non-Uniform intensity normalization) >Talairach transform computation >Intensity Normalization 1 >Skull Strip >EM Register (linear volumetric registration) >CA Intensity Normalization >CA Non-linear Volumetric Registration >Remove Neck >LTA with Skull >CA Label (Volumetric Labeling, ie Aseg) and Statistics >Intensity Normalization 2 (start here for control points) >White matter segmentation >Edit WM With ASeg >Fill (start here for wm edits) >Tessellation (begins per-hemisphere operations) >Smooth1 >Inflate1 >QSphere >Automatic Topology Fixer >Final Surfs (start here for brain edits for pial surf) >Smooth2 >Inflate2 >Spherical Mapping >Spherical Registration >Spherical Registration, Contralateral hemisphere >Map average curvature to subject >Cortical Parcellation - Desikan_Killiany and Christophe (Labeling) >Cortical Parcellation Statistics >Cortical Ribbon Mask >Cortical Parcellation mapping to Aseg > > BW > S Das > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei > [lzol...@nmr.mgh.harvard.edu] > Sent: 04 July 2017 22:04 > To: Freesurfer support list > Subject: Re: [Freesurfer] recon-all on newborn > > Hi S Das, > > We are trying to release the infant pipeline by the end of the summer. > > Lilla > > On Tue, 4 Jul 2017, Das S. wrote: > >> Dear Freesurfer expert, >> I want to perform recon-all pipeline on neonates data.Can I do so? >> I was going through some mail archives and there it is said that on T1 image >> of neonates data we can't perform recon-all. >> But again there is another paper where it says Freesurfer can perform >> segmentation of neonates image. >> Any input will be appreciated. >> Thanks >> S Das >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > 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 > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all on newborn
Thanks for the reply. If you let me know, among the below list of steps of current recon-all, currently which is not suitable to perform on neonates MRI image, will really appreciate. Autorecon Processing Stages: Motion Correction and Conform NU (Non-Uniform intensity normalization) Talairach transform computation Intensity Normalization 1 Skull Strip EM Register (linear volumetric registration) CA Intensity Normalization CA Non-linear Volumetric Registration Remove Neck LTA with Skull CA Label (Volumetric Labeling, ie Aseg) and Statistics Intensity Normalization 2 (start here for control points) White matter segmentation Edit WM With ASeg Fill (start here for wm edits) Tessellation (begins per-hemisphere operations) Smooth1 Inflate1 QSphere Automatic Topology Fixer Final Surfs (start here for brain edits for pial surf) Smooth2 Inflate2 Spherical Mapping Spherical Registration Spherical Registration, Contralateral hemisphere Map average curvature to subject Cortical Parcellation - Desikan_Killiany and Christophe (Labeling) Cortical Parcellation Statistics Cortical Ribbon Mask Cortical Parcellation mapping to Aseg BW S Das From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Lilla Zollei [lzol...@nmr.mgh.harvard.edu] Sent: 04 July 2017 22:04 To: Freesurfer support list Subject: Re: [Freesurfer] recon-all on newborn Hi S Das, We are trying to release the infant pipeline by the end of the summer. Lilla On Tue, 4 Jul 2017, Das S. wrote: > Dear Freesurfer expert, > I want to perform recon-all pipeline on neonates data.Can I do so? > I was going through some mail archives and there it is said that on T1 image > of neonates data we can't perform recon-all. > But again there is another paper where it says Freesurfer can perform > segmentation of neonates image. > Any input will be appreciated. > Thanks > S Das > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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
[Freesurfer] recon-all on newborn
Dear Freesurfer expert, I want to perform recon-all pipeline on neonates data.Can I do so? I was going through some mail archives and there it is said that on T1 image of neonates data we can't perform recon-all. But again there is another paper where it says Freesurfer can perform segmentation of neonates image. Any input will be appreciated. Thanks S Das ___ 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] Implement my own parcellation on aparc+aseg.mgz file
39 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 503144 Used brute-force search on 0 voxels relabeling unlikely voxels in interior of white matter average std[0] = 7.3 pass 1: 74 changed. pass 2: 4 changed. pass 3: 0 changed. nchanged = 0 Writing output aseg to /home/koushik/Parcellation/100307/mri/aparc+aseg.mgz #- #@# AParc-to-ASeg a2009s Mon Apr 10 22:21:48 BST 2017 /home/koushik/Parcellation/100307 INFO: skipping a2009s aparc2aseg #- #@# AParc-to-ASeg DKTatlas Mon Apr 10 22:21:48 BST 2017 /home/koushik/Parcellation/100307 INFO: skipping DKTatlas aparc2aseg Started at Mon Apr 10 22:18:54 BST 2017 Ended at Mon Apr 10 22:21:48 BST 2017 #@#%# recon-all-run-time-hours 0.048 recon-all -s 100307 finished without error at Mon Apr 10 22:21:48 BST 2017 *** Thanks & regards Sarbani From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 28 April 2017 18:14 To: Freesurfer support list Subject: Re: [Freesurfer] Implement my own parcellation on aparc+aseg.mgz file ok, then what is the next step in your processing? And where does it go wrong? Does the annot display in the proper colors on the surface? Sorry, I lost track of what was going on in your previous emails Bruce On Fri, 28 Apr 2017, Das S. wrote: > Yes there is embedded color file in my annot file. Here is the extract of > lh.aparc.annot that I created. > > koushik@koushik-DQ77MK:~/Parcellation/100307_old/100307/label$ mris_info > lh.aparc.annot > reading colortable from annotation file... > colortable with 95 entries read (originally > 100307/label/eq_parcellation_label/MyColorLUT.txt) > 0 unknown 130 18 340 > 1 node-lh-170 130 1800 > 2 node-lh-2 245 245 2450 > 3 node-lh-3 205 62 780 > 4 node-lh-4 120 18 1340 > 5 node-lh-5 196 58 2500 > 6 node-lh-6 0 148 00 > 7 node-lh-7 220 248 1640 > 8 node-lh-8 230 148 340 > 9 node-lh-9 0 118 140 > 10 node-lh-10 70 118 140 > 11 node-lh-11 122 186 2200 > 12 node-lh-12 236 13 1760 > 13 node-lh-13 12 48 2550 > 14 node-lh-14 204 182 1420 > 15 node-lh-15 42 204 1640 > 16 node-lh-16 119 159 1760 > 17 node-lh-17 220 216 200 > 18 node-lh-18 103 255 2550 > 19 node-lh-19 80 196 980 > 20 node-lh-20 60 58 2100 > 21 node-lh-21 160 58 2100 > 22 node-lh-22 120 58 2100 > 23 node-lh-23 40 58 2100 > 24 node-lh-24 60 120 600 > 25 node-lh-25 255 100 00 > 26 node-lh-26 250 165 00 > 27 node-lh-270 255 1270 > 28 node-lh-28 165 42 420 > 29 node-lh-29 135 206 2350 > 30 node-lh-30 160 32 2400 > 31 node-lh-310 200 2000 > 32 node-lh-32 100 50 1000 > 33 node-lh-33 135 50 740 > 34 node-lh-34 122 135 500 > 35 node-lh-35 51 50 1350 > 36 node-lh-36 74 155 600 > 37 node-lh-37 120 62 430 > 38 node-lh-38 74 155 600 > 39 node-lh-39 122 135 500 > 40 node-lh-40 100 120 500 > 41 node-rh-170 130 1800 > 42 node-rh-2 245 245 2450 > 43 node-rh-3 205 62 780 > 44 node-rh-4 120 18 1340 > 45 node-rh-5 196 58 2500 > 46 node-rh-6 0 148 00 &g
Re: [Freesurfer] Implement my own parcellation on aparc+aseg.mgz file
103 255 255 255 87 Left-Accumbens-area 255 165 0 255 88 Right-Thalamus-Proper 0 118 14 255 89 Right-Caudate 122 186 220 255 90 Right-Putamen 236 13 176 255 91 Right-Pallidum 13 48 255 255 92 Right-Hippocampus 220 216 20 255 93 Right-Amygdala 103 255 255 255 94 Right-Accumbens-area255 165 0 255 From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 28 April 2017 15:35 To: Freesurfer support list Subject: Re: [Freesurfer] Implement my own parcellation on aparc+aseg.mgz file Hi Das can you check if there is an embedded colormap in your .annot file?You can do this by running mris_info on it. cheers Bruce On Fri, 28 Apr 2017, Das S. wrote: > Hi > I have create my own annot file and lookuptable for cortical parcellation. > How I can implement my own parcellation in aparc+aseg.mgz file. > > I am also stuck on how to update the FreeSurferColorLUT.txt file? > > Please help. > Thanks > Sarbani > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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
[Freesurfer] Implement my own parcellation on aparc+aseg.mgz file
Hi I have create my own annot file and lookuptable for cortical parcellation. How I can implement my own parcellation in aparc+aseg.mgz file. I am also stuck on how to update the FreeSurferColorLUT.txt file? Please help. Thanks Sarbani ___ 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] debug mri_aparc2aseg
Hi I need to debug the issue I am facing at the moment. So I want to run the program with GDB. I could run it with gdb but no debug information/symbol is present in the current installed form. So I guess I need to recompile the mri_aparc2aseg program with in debug mode. Can you please help me in that? What is the easiest way to recompile with the debug symbols so that I can put a breakpoint in GDB? Also, if there any option to activate more logs/log levels? Thanks a lot for your help. Much appreciated. Regards, Sarbani ___ 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] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Hi Can you please explain what the flags mean here, I don't find them in help. mri_aparc2aseg --s 100307 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --s : subject --volmask : ? --aseg: ? --relabel: ? and what are the /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca and mri/aseg.auto_noCCseg.label_intensities.txt files? I am really stuck to put my colortable in aparc+aseg.mgz file. Please help. Thanks Sarbani From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Das S. [sarbani@soton.ac.uk] Sent: 28 April 2017 12:16 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table Hi If I use my colorLookup table in annot file, then will mri_aparc2aseg will update that in FreeSurfurColorLUT.txt table. I am just trying to understand how mri_aparc2aseg works seeing the below text the extracted from FreeSurferColorLUT.txt. Still the voxel in apar+aseg.mgh does not showing value from my parcellation table. Extract from FreesurferLUT.txt # Below is the color table for the cortical labels of the seg volume # created by mri_aparc2aseg in which the aseg cortex label is replaced # by the labels in the aparc. It also supports wm labels that will # eventually be created by mri_aparc2aseg. Otherwise, the aseg labels # do not change from above. The cortical lables are the same as in # colortable_desikan_killiany.txt, except that left hemisphere has # 1000 added to the index and the right has 2000 added. The label # names are also prepended with ctx-lh or ctx-rh. The white matter # labels are the same as in colortable_desikan_killiany.txt, except # that left hemisphere has 3000 added to the index and the right has # 4000 added. The label names are also prepended with wm-lh or wm-rh. # Centrum semiovale is also labled with 5001 (left) and 5002 (right). # Even further below are the color tables for aparc.a2005s and aparc.a2009s. Thanks Sarbani From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 27 April 2017 21:00 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table freeview -v norm.mgz aparc+aseg.mgh:colormap=lut should do the trick (or another volume) cheers Bruce On Thu, 27 Apr 2017, Das S. wrote: > How I can view the parcellation values from aparc+aseg.mgh file in freesurfer. > > > > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Das S. > [sarbani@soton.ac.uk] > Sent: 27 April 2017 20:22 > To: Freesurfer support list > Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value > from my parcellation table > > That's for sure a valuable input. I will follow the way you said and most > importantly change the output file name. > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: 27 April 2017 20:13 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value > from my parcellation table > > Try just running mri_aparc2aseg to do it directly from the annots you > create. You can look in recon-all.log for the command line that creates > the aparc+aseg.mgz and adapt it to your file names (make sure to change > the output so that you don't overwrite what is there > > > > On 04/27/2017 02:55 PM, Das S. wrote: >> Thanks for the reply. >> It has changed some way but not showing values from my lookup table. >> I was just following the convention of recon-all. >> Sarbani >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: 27 April 2017 19:34 >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value >> from my parcellation table >> >> Are you getting the same aparc+aseg.mgz or has it changed in some way, >> but not the way you wanted. BTW, you can create a aparc+aseg.mgz style >> output directly from the annots (not sure what the point of the gcs >> stuff is) >> >> >> On 04/27/2017 01:24 PM, Das S. wrote: >>> Dear Freesurfer Deve
Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Hi If I use my colorLookup table in annot file, then will mri_aparc2aseg will update that in FreeSurfurColorLUT.txt table. I am just trying to understand how mri_aparc2aseg works seeing the below text the extracted from FreeSurferColorLUT.txt. Still the voxel in apar+aseg.mgh does not showing value from my parcellation table. Extract from FreesurferLUT.txt # Below is the color table for the cortical labels of the seg volume # created by mri_aparc2aseg in which the aseg cortex label is replaced # by the labels in the aparc. It also supports wm labels that will # eventually be created by mri_aparc2aseg. Otherwise, the aseg labels # do not change from above. The cortical lables are the same as in # colortable_desikan_killiany.txt, except that left hemisphere has # 1000 added to the index and the right has 2000 added. The label # names are also prepended with ctx-lh or ctx-rh. The white matter # labels are the same as in colortable_desikan_killiany.txt, except # that left hemisphere has 3000 added to the index and the right has # 4000 added. The label names are also prepended with wm-lh or wm-rh. # Centrum semiovale is also labled with 5001 (left) and 5002 (right). # Even further below are the color tables for aparc.a2005s and aparc.a2009s. Thanks Sarbani From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 27 April 2017 21:00 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table freeview -v norm.mgz aparc+aseg.mgh:colormap=lut should do the trick (or another volume) cheers Bruce On Thu, 27 Apr 2017, Das S. wrote: > How I can view the parcellation values from aparc+aseg.mgh file in freesurfer. > > > > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Das S. > [sarbani@soton.ac.uk] > Sent: 27 April 2017 20:22 > To: Freesurfer support list > Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value > from my parcellation table > > That's for sure a valuable input. I will follow the way you said and most > importantly change the output file name. > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: 27 April 2017 20:13 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value > from my parcellation table > > Try just running mri_aparc2aseg to do it directly from the annots you > create. You can look in recon-all.log for the command line that creates > the aparc+aseg.mgz and adapt it to your file names (make sure to change > the output so that you don't overwrite what is there > > > > On 04/27/2017 02:55 PM, Das S. wrote: >> Thanks for the reply. >> It has changed some way but not showing values from my lookup table. >> I was just following the convention of recon-all. >> Sarbani >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: 27 April 2017 19:34 >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value >> from my parcellation table >> >> Are you getting the same aparc+aseg.mgz or has it changed in some way, >> but not the way you wanted. BTW, you can create a aparc+aseg.mgz style >> output directly from the annots (not sure what the point of the gcs >> stuff is) >> >> >> On 04/27/2017 01:24 PM, Das S. wrote: >>> Dear Freesurfer Developer, >>> I am using freesurfer to create a equal zone parcellation on cortical >>> surface. >>> I have used recon-all steps to create the aparc+aseg.mgz file. But in my >>> aparc+aseg.mgz file I can't see the equal parcellation I have done. >>> >>> Here are steps that I have followed: >>> >>>1. Divided the vertex point from the sphere.reg into equal numbers and >>> assigned them to label files.This way I have created n number of label >>> files, n/2 for left and n/2 for right sphere. The label file names are as >>> below lh.node-lh-1.label >>> >>> 2. Then I run the mris_label2annot command to create the >>> ?h.free40aparc.annot files. Before that I have created two color lookup >>> table for left and right hemisphere. >&
Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
How I can view the parcellation values from aparc+aseg.mgh file in freesurfer. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Das S. [sarbani@soton.ac.uk] Sent: 27 April 2017 20:22 To: Freesurfer support list Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table That's for sure a valuable input. I will follow the way you said and most importantly change the output file name. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 27 April 2017 20:13 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table Try just running mri_aparc2aseg to do it directly from the annots you create. You can look in recon-all.log for the command line that creates the aparc+aseg.mgz and adapt it to your file names (make sure to change the output so that you don't overwrite what is there On 04/27/2017 02:55 PM, Das S. wrote: > Thanks for the reply. > It has changed some way but not showing values from my lookup table. > I was just following the convention of recon-all. > Sarbani > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: 27 April 2017 19:34 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value > from my parcellation table > > Are you getting the same aparc+aseg.mgz or has it changed in some way, > but not the way you wanted. BTW, you can create a aparc+aseg.mgz style > output directly from the annots (not sure what the point of the gcs > stuff is) > > > On 04/27/2017 01:24 PM, Das S. wrote: >> Dear Freesurfer Developer, >> I am using freesurfer to create a equal zone parcellation on cortical >> surface. >> I have used recon-all steps to create the aparc+aseg.mgz file. But in my >> aparc+aseg.mgz file I can't see the equal parcellation I have done. >> >> Here are steps that I have followed: >> >>1. Divided the vertex point from the sphere.reg into equal numbers and >> assigned them to label files.This way I have created n number of label >> files, n/2 for left and n/2 for right sphere. The label file names are as >> below lh.node-lh-1.label >> >> 2. Then I run the mris_label2annot command to create the >> ?h.free40aparc.annot files. Before that I have created two color lookup >> table for left and right hemisphere. >> >> >> mris_label2annot --s 100307 --h rh --no-unknown --ctab >> 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc >> --ldir 100307/label/eq_parcellation_label/right >> >>mris_label2annot --s 100307 --h lh --no-unknown --ctab >> 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc >> --ldir 100307/label/eq_parcellation_label/left >> >> Content of ColorLUT.txt >> 801 node-lh-170 130 180 0 >> 802 node-lh-2 245 245 245 0 >> 803 node-lh-3205 62 78 0. >> >> 3. Then I am using the mris_ca_train to create the .gcs file. >> >> mris_ca_train -t >> 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh >> 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 >> 100307/label/lh.leftaparc.gcs >> >> >>mris_ca_train -t >> 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh >> 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 >> 100307/label/rh.righttaparc.gcs >> >> 4. then I am following the recon-all steps and call the mris_ca_label >> command as below: >> mris_ca_label -t >> 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh >> 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs >> 100307/label/rh.aparc.annot >> mris_ca_label -t >> 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh >> 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs >> 100307/label/lh.aparc.annot >> >> 5. Then I followed the rest of recon-all steps to create the apar+aseg.mgz >> file as below: >> recon-all -pial -subjid 100307 >> recon-all -cortribbon -subjid 100307 >> recon-all -parcstats
Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
That's for sure a valuable input. I will follow the way you said and most importantly change the output file name. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 27 April 2017 20:13 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table Try just running mri_aparc2aseg to do it directly from the annots you create. You can look in recon-all.log for the command line that creates the aparc+aseg.mgz and adapt it to your file names (make sure to change the output so that you don't overwrite what is there On 04/27/2017 02:55 PM, Das S. wrote: > Thanks for the reply. > It has changed some way but not showing values from my lookup table. > I was just following the convention of recon-all. > Sarbani > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: 27 April 2017 19:34 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value > from my parcellation table > > Are you getting the same aparc+aseg.mgz or has it changed in some way, > but not the way you wanted. BTW, you can create a aparc+aseg.mgz style > output directly from the annots (not sure what the point of the gcs > stuff is) > > > On 04/27/2017 01:24 PM, Das S. wrote: >> Dear Freesurfer Developer, >> I am using freesurfer to create a equal zone parcellation on cortical >> surface. >> I have used recon-all steps to create the aparc+aseg.mgz file. But in my >> aparc+aseg.mgz file I can't see the equal parcellation I have done. >> >> Here are steps that I have followed: >> >>1. Divided the vertex point from the sphere.reg into equal numbers and >> assigned them to label files.This way I have created n number of label >> files, n/2 for left and n/2 for right sphere. The label file names are as >> below lh.node-lh-1.label >> >> 2. Then I run the mris_label2annot command to create the >> ?h.free40aparc.annot files. Before that I have created two color lookup >> table for left and right hemisphere. >> >> >> mris_label2annot --s 100307 --h rh --no-unknown --ctab >> 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc >> --ldir 100307/label/eq_parcellation_label/right >> >>mris_label2annot --s 100307 --h lh --no-unknown --ctab >> 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc >> --ldir 100307/label/eq_parcellation_label/left >> >> Content of ColorLUT.txt >> 801 node-lh-170 130 180 0 >> 802 node-lh-2 245 245 245 0 >> 803 node-lh-3205 62 78 0. >> >> 3. Then I am using the mris_ca_train to create the .gcs file. >> >> mris_ca_train -t >> 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh >> 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 >> 100307/label/lh.leftaparc.gcs >> >> >>mris_ca_train -t >> 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh >> 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 >> 100307/label/rh.righttaparc.gcs >> >> 4. then I am following the recon-all steps and call the mris_ca_label >> command as below: >> mris_ca_label -t >> 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh >> 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs >> 100307/label/rh.aparc.annot >> mris_ca_label -t >> 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh >> 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs >> 100307/label/lh.aparc.annot >> >> 5. Then I followed the rest of recon-all steps to create the apar+aseg.mgz >> file as below: >> recon-all -pial -subjid 100307 >> recon-all -cortribbon -subjid 100307 >> recon-all -parcstats -subjid 100307 >> recon-all -pctsurfcon -subjid 100307 >> recon-all -hyporelabel -subjid 100307 >> recon-all -aparc2aseg -subjid 100307 >> >> >> I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong >> that the file is not reflecting valueof my equal parcellation lookup table. >> I tried many ways but coundn't figure out. Any help will be much appreciated. >> Thanks >> Sarba
Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table
Thanks for the reply. It has changed some way but not showing values from my lookup table. I was just following the convention of recon-all. Sarbani From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 27 April 2017 19:34 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] the voxel in apar+aseg.mgh does not showing value from my parcellation table Are you getting the same aparc+aseg.mgz or has it changed in some way, but not the way you wanted. BTW, you can create a aparc+aseg.mgz style output directly from the annots (not sure what the point of the gcs stuff is) On 04/27/2017 01:24 PM, Das S. wrote: > Dear Freesurfer Developer, > I am using freesurfer to create a equal zone parcellation on cortical surface. > I have used recon-all steps to create the aparc+aseg.mgz file. But in my > aparc+aseg.mgz file I can't see the equal parcellation I have done. > > Here are steps that I have followed: > > 1. Divided the vertex point from the sphere.reg into equal numbers and > assigned them to label files.This way I have created n number of label files, > n/2 for left and n/2 for right sphere. The label file names are as below > lh.node-lh-1.label > > 2. Then I run the mris_label2annot command to create the ?h.free40aparc.annot > files. Before that I have created two color lookup table for left and right > hemisphere. > > > mris_label2annot --s 100307 --h rh --no-unknown --ctab > 100307/label/eq_parcellation_label/right/MyColorLUTright.txt --a rightaparc > --ldir 100307/label/eq_parcellation_label/right > > mris_label2annot --s 100307 --h lh --no-unknown --ctab > 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt --a leftaparc > --ldir 100307/label/eq_parcellation_label/left > > Content of ColorLUT.txt > 801 node-lh-170 130 180 0 > 802 node-lh-2 245 245 245 0 > 803 node-lh-3205 62 78 0. > > 3. Then I am using the mris_ca_train to create the .gcs file. > >mris_ca_train -t > 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt lh > 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.annot 100307 > 100307/label/lh.leftaparc.gcs > > > mris_ca_train -t > 100307/label/eq_parcellation_label/right/MyColorLUTright.txt rh > 100307/surf/rh.sphere.reg 100307/label/rh.rightaparc.annot 100307 > 100307/label/rh.righttaparc.gcs > > 4. then I am following the recon-all steps and call the mris_ca_label command > as below: >mris_ca_label -t > 100307/label/eq_parcellation_label/right/MyColorLUTright.txt 100307 rh > 100307/surf/rh.sphere.reg 100307/label/rh.righttaparc.gcs > 100307/label/rh.aparc.annot >mris_ca_label -t > 100307/label/eq_parcellation_label/left/MyColorLUTleft01.txt 100307 lh > 100307/surf/lh.sphere.reg 100307/label/lh.leftaparc.gcs > 100307/label/lh.aparc.annot > > 5. Then I followed the rest of recon-all steps to create the apar+aseg.mgz > file as below: >recon-all -pial -subjid 100307 >recon-all -cortribbon -subjid 100307 >recon-all -parcstats -subjid 100307 >recon-all -pctsurfcon -subjid 100307 >recon-all -hyporelabel -subjid 100307 >recon-all -aparc2aseg -subjid 100307 > > > I am attaching my aparc+aseg.mgh file. Please guide me where I did wrong that > the file is not reflecting valueof my equal parcellation lookup table. I > tried many ways but coundn't figure out. Any help will be much appreciated. > Thanks > Sarbani Das > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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
Re: [Freesurfer] mris_label2annot not creating annot file
Thanks the problem is resolved now. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Das S. [sarbani@soton.ac.uk] Sent: 21 April 2017 15:47 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_label2annot not creating annot file Hi, I was using the mris_label2annot to create .annot file before but now couldn't figure out why the .annot file is not being created. The mris_label2annot is giving the below output but not creating the label files. My label file names are as node-lh-xx.label and the content of ctab file as below: 0 node-lh-0 25 5 25 0 1 node-lh-1 70 0 180 0 2 node-lh-2 245 245 245 0 3 node-lh-3 205 62 78 0 4 node-lh-4 120 18 134 0 5 node-lh-5 196 58 250 0 6 node-lh-6 0 148 0 0 7 node-lh-7 220 248 164 0 8 node-lh-8 230 148 34 0 9 node-lh-9 0 118 14 0 10 node-lh-10 70 118 14 0 11 node-lh-11 122 186 220 0 12 node-lh-12 236 13 176 0 13 node-lh-13 12 48 255 0 14 node-lh-14 204 182 142 0 *** mris_label2annot --s 100307 --h lh --no-unknown --ctab label/eq_parcellation_label/MyColorLUTleft01.txt --a eq40left --ldir label/eq_parcellation_label/left/ Reading ctab label/eq_parcellation_label/MyColorLUTleft01.txt Number of ctab entries 41 INFO: no labels specified, generating from ctab $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/koushik/Parcellation/100307 cmdline mris_label2annot --s 100307 --h lh --no-unknown --ctab label/eq_parcellation_label/MyColorLUTleft01.txt --a eq40left --ldir label/eq_parcellation_label/left/ sysname Linux hostname koushik-DQ77MK machine x86_64 user koushik subject 100307 hemilh SUBJECTS_DIR /home/koushik/Parcellation ColorTable label/eq_parcellation_label/MyColorLUTleft01.txt AnnotName eq40left nlables 0 LabelThresh 0 0.00 Loading /home/koushik/Parcellation/100307/surf/lh.orig Writing annot to /home/koushik/Parcellation/100307/label/lh.eq40left.annot Thanks Sarbani ___ 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
[Freesurfer] mris_label2annot not creating annot file
Hi, I was using the mris_label2annot to create .annot file before but now couldn't figure out why the .annot file is not being created. The mris_label2annot is giving the below output but not creating the label files. My label file names are as node-lh-xx.label and the content of ctab file as below: 0 node-lh-0 25 5 25 0 1 node-lh-1 70 0 180 0 2 node-lh-2 245 245 245 0 3 node-lh-3 205 62 78 0 4 node-lh-4 120 18 134 0 5 node-lh-5 196 58 250 0 6 node-lh-6 0 148 0 0 7 node-lh-7 220 248 164 0 8 node-lh-8 230 148 34 0 9 node-lh-9 0 118 14 0 10 node-lh-10 70 118 14 0 11 node-lh-11 122 186 220 0 12 node-lh-12 236 13 176 0 13 node-lh-13 12 48 255 0 14 node-lh-14 204 182 142 0 *** mris_label2annot --s 100307 --h lh --no-unknown --ctab label/eq_parcellation_label/MyColorLUTleft01.txt --a eq40left --ldir label/eq_parcellation_label/left/ Reading ctab label/eq_parcellation_label/MyColorLUTleft01.txt Number of ctab entries 41 INFO: no labels specified, generating from ctab $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /home/koushik/Parcellation/100307 cmdline mris_label2annot --s 100307 --h lh --no-unknown --ctab label/eq_parcellation_label/MyColorLUTleft01.txt --a eq40left --ldir label/eq_parcellation_label/left/ sysname Linux hostname koushik-DQ77MK machine x86_64 user koushik subject 100307 hemilh SUBJECTS_DIR /home/koushik/Parcellation ColorTable label/eq_parcellation_label/MyColorLUTleft01.txt AnnotName eq40left nlables 0 LabelThresh 0 0.00 Loading /home/koushik/Parcellation/100307/surf/lh.orig Writing annot to /home/koushik/Parcellation/100307/label/lh.eq40left.annot Thanks Sarbani ___ 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] mris_ca_label giving error CTABfindAnnotation: ct was NULL
Thanks . Its working now. ___T_ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 11 April 2017 16:48 To: Freesurfer support list Subject: Re: [Freesurfer] mris_ca_label giving error CTABfindAnnotation: ct was NULL when you run mris_ca_train use -t and it will embed it in the .gcs file On Tue, 11 Apr 2017, Das S. wrote: > Hi, > I have created a color table, an annot file and a .gcs file( attached with > the mail). > But when I am trying to execute mris_ca_label with my own .gcs file I am > getting the error : > > mris_ca_label -l 100307/label/lh.cortex.label -aseg > 100307/mri/aseg.presurf.mgz 100307 lh lh.sphere.reg > 100307/label/lh.eq40aparc.gcs lh.aparc.annot > using 100307/mri/aseg.presurf.mgz aseg volume to correct midline > $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ > $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ > reading atlas from 100307/label/lh.eq40aparc.gcs... > average std = 0.2 using min determinant for regularization = 0.001 > 0 singular and 185 ill-conditioned covariance matrices regularized > input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature > labeling surface... > CTABfindAnnotation: ct was NULL > No such file or directory > CTABfindAnnotation: ct was NULL > No such file or directory > CTABfindAnnotation: ct was NULL > No such file or directory > > . > > Before this I have used the below commands, to sucessfully create the .annot > and .gcs file: > 1. To create .annot file from label files and CTAB file-- > mris_label2annot --s 100307 --h lh --no-unknown --ctab > 100307/label/eq_parcellation_label/MyColorLUT.txt --a eq40aparc --ldir > 100307/label/eq_parcellation_label > > 2. To crate .gcs file from annot file. > mris_ca_train rh 100307/surf/rh.sphere 100307/label/rh.eq40aparc.annot 100307 > 100307/label/rh.eq40aparc.gcs > > I am not be able to understand where is the problem. > Any help will be appreciated. > Thanks > Sarbani > ___ 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
[Freesurfer] Error during recon-all
Dear FreeSurfer Developers, I was trying to use the command recon-all -autorecon1 -subjid bert and got an error. When I checked I found the error was coming while executing the below command: nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50 When I executed the command separately I got below error message: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Can you please suggest why the error is coming and how to remove it. Many thanks Sarbani ___ 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] ERROR: nu_correct
Dear Freesurfer Developers, I was trying to use the recon-all -autorecon1 -subjid bert and got an error. When I checked I found the error was coming while executing the below command: nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc ./tmp.mri_nu_correct.mni.7555/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.7555/0/ -iterations 1000 -distance 50 When I executed the command separately I got below error message: Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct Can you please suggest why the error is coming and how to remove it. Many thanks Sarbani ___ 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.
