Re: [Freesurfer] extract pial surface
The area.pial file. Best, Feng 发件人：Sandy Schramm 发送时间：2015-11-06 15:24 主题：[Freesurfer] extract pial surface 收件人："freesurfer" 抄送： Dear experts, how can I extract pial surface (in mm2) of all our participants? Performing aparcstats2table -meas area extracts white area. Thanks, Sandy ___ 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 fsgd file
hi, Bronwyn You should change the position of parameter "dods" like this: mri_glmfit --fsgd long-2stage_ConAR.fsgd dods --glmdir long-2stage_ConAR.area.lh.spc.glmdir --y long-ConAR.lh.area-spc.stack.fwhm10.mgh Hope this helps. Best, Feng 发件人：Bronwyn Overs 发送时间：2015-10-14 08:11 主题：[Freesurfer] Problem with fsgd file 收件人："Freesurfer support list" 抄送： Dear mailing list, I am trying to run a longitudinal 2 stage model using mri_glmfit. Here is the command I am using: mri_glmfit --fsgd long-2stage_ConAR.fsgd --glmdir long-2stage_ConAR.area.lh.spc.glmdir --y long-ConAR.lh.area-spc.stack.fwhm10.mgh dods --C me_age-all.mtx --C me_gender.mtx --C me_group.mtx --C int_ageXgroup.mtx --C int_ageXgender.mtx --C int_genderXgroup.mtx --C int_ageXgenderXgroup.mtx --surf fsaverage lh --label long-ConAR.lh.area.fsaverage.cortex.label However, when I try to run the command it has problems reading my fsgd file. I have attached my file for reference and here are the errors it spits out: gdfReadHeader: reading long-2stage_ConAR.fsgd INFO: ignoring tag 7541001001 INFO: ignoring tag 7541002001 INFO: ignoring tag 7541003001 INFO: ignoring tag 7541006001 INFO: ignoring tag 7541009001 INFO: ignoring tag 7541011004 INFO: ignoring tag 7541012004 INFO: ignoring tag 7541017001 INFO: ignoring tag 7541018001 INFO: ignoring tag 7541020001 INFO: ignoring tag 7541022001 INFO: ignoring tag 7541023001 INFO: ignoring tag 7541024001 INFO: ignoring tag 7541026001 INFO: ignoring tag 7541030001 INFO: ignoring tag 7541031001 INFO: ignoring tag 7541036001 INFO: ignoring tag 7541040001 INFO: ignoring tag 7541041001 INFO: ignoring tag 7541042001 INFO: ignoring tag 7541044001 INFO: ignoring tag 7541046001 INFO: ignoring tag 7541047001 INFO: ignoring tag 7541048004 INFO: ignoring tag 7541049001 INFO: ignoring tag 7541052001 INFO: ignoring tag 7541055001 INFO: ignoring tag 7541057001 INFO: ignoring tag 7541058001 INFO: ignoring tag 7541059001 INFO: ignoring tag 7541060001 INFO: ignoring tag 7541062001 INFO: ignoring tag 7541070001 INFO: ignoring tag 7541075001 INFO: ignoring tag 7541078001 INFO: ignoring tag 7541080001 INFO: ignoring tag 7541084001 INFO: ignoring tag 7541085001 INFO: ignoring tag 7541088001 INFO: ignoring tag 7541090001 INFO: ignoring tag 7541093001 INFO: ignoring tag 7541094001 INFO: ignoring tag 7541096001 INFO: ignoring tag 7541097004 INFO: ignoring tag 7541099001 INFO: ignoring tag 754111 INFO: ignoring tag 7541101001 INFO: ignoring tag 7541102001 INFO: ignoring tag 7541103001 INFO: ignoring tag 7541106001 INFO: ignoring tag 7541108001 INFO: ignoring tag 7541110004 INFO: ignoring tag 7541112001 INFO: ignoring tag 7541114001 INFO: ignoring tag 7541116001 INFO: ignoring tag 7541118001 INFO: ignoring tag 7541119001 INFO: ignoring tag 7541120001 INFO: ignoring tag 7541124001 INFO: ignoring tag 7541125001 INFO: ignoring tag 7541132004 INFO: ignoring tag 7541133001 INFO: ignoring tag 7541139001 INFO: ignoring tag 7541142001 INFO: ignoring tag 7541143001 INFO: ignoring tag 7541146001 INFO: ignoring tag 7541149001 INFO: ignoring tag 7541150001 INFO: ignoring tag 7541151001 INFO: ignoring tag 7541156001 INFO: ignoring tag 7541161001 INFO: ignoring tag 7541165001 INFO: ignoring tag 7541168001 INFO: ignoring tag 7541175001 INFO: ignoring tag 7541177001 INFO: ignoring tag 7541178001 INFO: ignoring tag 7541182001 INFO: ignoring tag 7541185001 INFO: ignoring tag 7541188001 INFO: ignoring tag 7541190004 INFO: ignoring tag 7541192004 INFO: ignoring tag 7541196001 INFO: ignoring tag 7541198001 INFO: ignoring tag 7541209001 INFO: ignoring tag 7541223001 INFO: ignoring tag 7541227001 INFO: ignoring tag 7541334001 INFO: ignoring tag 7541337001 INFO: ignoring tag 7541345001 INFO: ignoring tag 7541346001 INFO: ignoring tag 7541353001 INFO: ignoring tag 7541366001 INFO: ignoring tag 7541378001 INFO: ignoring tag 7541383001 INFO: ignoring tag 7541388001 INFO: ignoring tag 7541391001 INFO: ignoring tag 7541396001 INFO: ignoring tag 754141 INFO: ignoring tag 7541401001 INFO: ignoring tag 7541402001 INFO: ignoring tag 7541409001 INFO: ignoring tag 7541411001 INFO: ignoring tag 7541412001 INFO: ignoring tag 7541421001 INFO: ignoring tag 7541442004 INFO: ignoring tag 7541443001 INFO: ignoring tag 7541445001 WARNING: gdfReadV1: class genderM-groupCtl is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 years -nan -nan 1 age_mc -nan -nan Class Means of each Continuous Variable 1 genderM-groupCtl -nan -nan 2 genderF-groupCtl -nan -nan 3 genderM-groupAR -nan -nan 4 genderF-groupAR -nan -nan INFO: gd2mtx_method is dods ERROR: Option dods unknown Can you tell me what is wrong? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW
[Freesurfer] A potential problem in qdec
Dear Freesurfer users, Is there anyone that use virtual box freesurfer version for group comparison via qdec? I use the freesurfer version below: VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G I used qdec for group comparison, but there was an error (acctached error.png) that puzzled me for a long time. I and my colleague help me to check all the files but do not find where is the error. I performed the same analyses on other computers, there was the same error. However, if I remove the files gender.levels, group.levels and fsid.levels (I means that I just keep the qdec.table.dat), it works. I can design, display and finally obtain the results. Could anyone give me some suggestions? Any help would be greatly appreciate. Best, Feng fsid.levels Description: Binary data gender.levels Description: Binary data group.levels Description: Binary data qdec.table.dat Description: Binary data ___ 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] A potential problem in qdec
Dear Freesurfer users, Is there anyone that use virtual box freesurfer version for group comparison via qdec? I use the freesurfer version below: VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G I used qdec for group comparison, but there was an error (acctached error.png) that puzzled me for a long time. I and my colleague help me to check all the files but do not find where is the error. However, if I remove the files gender.levels, group.levels and fsid.levels (I means that I just keep the qdec.table.dat), it works. I can design, display and finally obtain the results. Could anyone give me some suggestions? Any help would be greatly appreciate. Best, Feng fsid.levels Description: Binary data gender.levels Description: Binary data group.levels Description: Binary data qdec.table.dat Description: Binary data ___ 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 in qdec
Dear Freesurfer experts, I used qdec for group comparison, but there is error (acctached error.png). I check all the files but do not find where is the erros. Could anyone give me some suggestions? Best, Feng fsid.levels Description: Binary data gender.levels Description: Binary data group.levels Description: Binary data qdec.table.dat Description: Binary data ___ 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] Query about the calculation of surface area
I thought that we calculate the Surface area, MeanCurv, GausCurv, FoldInd and CurvInd in each vertex, and thus we can obtain the whole map on the surface. Subsequently, using the predefined atlas, we can further obtain the mean and std value in each brain region (because each vertex has a value). It looks like you do not calculate surface area and other measures in the aforementioned way, right? From your words, it may be that the surface area is the summation of each vertex's area in each region, right? In contrast, for thickness, you compute the mean thickness across all the vertics. And of coz, I can compute the total thickness in each region like the area (summation of each vertex's thickness in each region), right? Best, Feng 发件人：Bruce Fischl 发送时间：2015-10-07 22:32 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list" 抄送： Hi Feng they are slightly different measures so which one you use really depends on your biological hypothesis. For thickness there are multiple measures within each ROI but only one area (that of the whole ROI), so mean and std doesn't make sense. cheers Bruce On Wed, 7 Oct 2015, chenhf_uestc wrote: > Thanks a lot, Bruce > > If I want to compare the surface area between the patients and healthy > control groups, which area file should I use? The area or the area.pial? Or > I should compare both of them? If I should use both, is there any > possibility that I would obtain different results from area and area.pial? I > mean, in this case, a brain region has significantly different area but same > (not significant) area.pial. How can I explain them in my research paper? > > BTW, just out of curiosity, in the stats file such as lh.aparc.stats, why > just thickness has the mean and std value, but other measures do not have > the std value? > SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd > > Best, > Feng > > > 发件人：Bruce Fischl > 发送时间：2015-10-06 20:45 > 主题：Re: [Freesurfer] Query about the calculation of surface area > 收件人："Freesurfer support list" > 抄送： > > yes, that is correct > Bruce > > > On Tue, 6 Oct 2015, chenhf_uestc wrote: > > > Thanks, Bruce So, in the stats folder of each subject, the > > lh.aparc.a2009s.stats file provides surfarea of each region. This value ?? ?> is the area for the white surface, right? > > Is the area of each vertex obtained by the average the area of triangles ?? ?su > > rrounding the vertex?Best, Feng > > > > _ > ___ > > 发件人：Bruce Fischl > > 发送时间：2015-10-06 20:25 > > 主题：Re: [Freesurfer] Query about the calculation of surface area > > 收件人："Freesurfer support list" > > 抄送： > > > > Hi Feng > > > > we compute the surface area of each surface and store it separately. The ?? ? > > ?h.area files are for the white surface and the ?h.area.pial for the pial > > > > > cheers > > Bruce > > On > > Tue, 6 Oct 2015, chenhf_uestc wrote: > > > > > Dear Freesurfer experts, > > > > > > I have a question about the calculation of surface area. The cortical ?? ?> > thickness is the distance between the pial and white matter. But, what ?? ?ab > > out > > > the surface area? Calculation based on pial or white matter? Or average > t > > he > > > area of both of them. > > > > > > Is the area of each vertex obtained by the average the area of triangle > s > ?? ?> surrounding the vertex? > > > In addition, where can I find the definition of meancurv, gauscurv, fol > di > > nd, > > > curvind? I do not find it in the fswiki. > > > > > > Best, > > > Feng > > > > > > > > > > > ___ > > 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 > i > > s > > addressed. If you believe this e-mail was sent to you in error and the e- > ma > > il > > contains patient information, please contact the Partners Compliance Help > Li > > ne at > > http://www.partners.org/complianceline . If the
Re: [Freesurfer] Questions about the correction methods in Surfstat
I see. Thanks a lot, Donald Best, Feng 发件人："MCLAREN, Donald" 发送时间：2015-10-07 11:01 主题：Re: [Freesurfer] Questions about the correction methods in Surfstat 收件人："Freesurfer support list" 抄送： >The output figure is attached. In the colorbar of the figure, left represents >cluster corrected p value and right one represents the vertex >corrected p >value, right? Right. >So, the warm color region in the figure can be survived by the RFT vertex >correction, and the cool color region in the figure can be >survived by the >RFT cluster correction, right? Right. RFT vertex correction is not a correct definition, it is a RFT correction based on the maximum peak in contrast with the larger cluster extent approach. >If so, the regions with either warm or cool color region that can be survived >after correction. When I report the results, I can report the >regions with >warm color (vertex level correction) or report the regions with cool color >(cluster level correction), right? Both thresholdings can be reported but I prefer peak thresholds (warm colors) due to the lack of spatial specificity with clustering thresholds. >In addtion, how can I understand the region overlapped by the warm and cool >color (like he postier cingulate cortex), can >simultaneously pass double >correction of vertex level and cluster level? It is not a double corrections. The figure simply shows two different RFT thresholding approaches. The final question is about the RFT cluster correction method, in the SPM or other software (like REST). Generally, on the cluster level correction, you should be based on a voxel (vertex) uncorrected height threshold of e.g. p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05, right? What is the detailed correction procedure in the Surfstat software? Exactly the same, p=0.001 for defining supra-threshold clusters and p=0.05 for RFT correction. Regards, Felix. Best Regards, Donald McLaren, PhD On Sun, Sep 13, 2015 at 9:36 AM, chenhf_uestc wrote: Dear Surfstat Users, I have a question about the RFT correction method in the Surfstat(http://www.math.mcgill.ca/keith/surfstat/). In the online manual, the command to perform RFT correction is as follows: [ pval, peak, clus ] = SurfStatP( slm, mask ); pval.P contains P-values for peaks, and pval.C contains P-values for clusters. This special structure is recognised by SurfStatView which draws the figure in a special way: SurfStatView( pval, avsurf, 'Males-females removing age' ); The output figure is attached. In the colorbar of the figure, left represents cluster corrected p value and right one represents the vertex corrected p value, right? So, the warm color region in the figure can be survived by the RFT vertex correction, and the cool color region in the figure can be survived by the RFT cluster correction, right? If so, the regions with either warm or cool color region that can be survived after correction. When I report the results, I can report the regions with warm color (vertex level correction) or report the regions with cool color (cluster level correction), right? In addtion, how can I understand the region overlapped by the warm and cool color (like he postier cingulate cortex), can simultaneously pass double correction of vertex level and cluster level? The final question is about the RFT cluster correction method, in the SPM or other software (like REST). Generally, on the cluster level correction, you should be based on a voxel (vertex) uncorrected height threshold of e.g. p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05, right? What is the detailed correction procedure in the Surfstat software? Any help would be greatly appreciate. Best, Feng ___ 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] Query about the calculation of surface area
Thanks a lot, Bruce If I want to compare the surface area between the patients and healthy control groups, which area file should I use? The area or the area.pial? Or I should compare both of them? If I should use both, is there any possibility that I would obtain different results from area and area.pial? I mean, in this case, a brain region has significantly different area but same (not significant) area.pial. How can I explain them in my research paper? BTW, just out of curiosity, in the stats file such as lh.aparc.stats, why just thickness has the mean and std value, but other measures do not have the std value? SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd Best, Feng 发件人：Bruce Fischl 发送时间：2015-10-06 20:45 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list" 抄送： yes, that is correct Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote: > Thanks, Bruce So, in the stats folder of each subject, the > lh.aparc.a2009s.stats file provides surfarea of each region. This value > is the area for the white surface, right? > Is the area of each vertex obtained by the average the area of triangles su > rrounding the vertex?Best, Feng > > > 发件人：Bruce Fischl > 发送时间：2015-10-06 20:25 > 主题：Re: [Freesurfer] Query about the calculation of surface area > 收件人："Freesurfer support list" > 抄送： > > Hi Feng > > we compute the surface area of each surface and store it separately. The > ?h.area files are for the white surface and the ?h.area.pial for the pial > > cheers > Bruce > On > Tue, 6 Oct 2015, chenhf_uestc wrote: > > > Dear Freesurfer experts, > > > > I have a question about the calculation of surface area. The cortical > > thickness is the distance between the pial and white matter. But, what ab > out > > the surface area? Calculation based on pial or white matter? Or average t > he > > area of both of them. > > > > Is the area of each vertex obtained by the average the area of triangles ?? ?> surrounding the vertex? > > In addition, where can I find the definition of meancurv, gauscurv, foldi > nd, > > curvind? I do not find it in the fswiki. > > > > Best, > > Feng > > > > > > > ___ > 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 i > s > addressed. If you believe this e-mail was sent to you in error and the e-ma > il > contains patient information, please contact the Partners Compliance HelpLi > ne at > http://www.partners.org/complianceline . If the e-mail was sent to you in e > rror > but does not contain patient information, please contact the sender and pro > perly > 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.
Re: [Freesurfer] Query about the calculation of surface area
Thanks, Bruce So, in the stats folder of each subject, the lh.aparc.a2009s.stats file provides surfarea of each region. This value is the area for the white surface, right? Is the area of each vertex obtained by the average the area of triangles surrounding the vertex? Best, Feng 发件人：Bruce Fischl 发送时间：2015-10-06 20:25 主题：Re: [Freesurfer] Query about the calculation of surface area 收件人："Freesurfer support list" 抄送： Hi Feng we compute the surface area of each surface and store it separately. The ?h.area files are for the white surface and the ?h.area.pial for the pial cheers Bruce On Tue, 6 Oct 2015, chenhf_uestc wrote: > Dear Freesurfer experts, > > I have a question about the calculation of surface area. The cortical > thickness is the distance between the pial and white matter. But, what about > the surface area? Calculation based on pial or white matter? Or average the > area of both of them. > > Is the area of each vertex obtained by the average the area of triangles > surrounding the vertex? > In addition, where can I find the definition of meancurv, gauscurv, foldind, > curvind? I do not find it in the fswiki. > > Best, > Feng > > > ___ 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] Query about the calculation of surface area
Dear Freesurfer experts, I have a question about the calculation of surface area. The cortical thickness is the distance between the pial and white matter. But, what about the surface area? Calculation based on pial or white matter? Or average the area of both of them. Is the area of each vertex obtained by the average the area of triangles surrounding the vertex? In addition, where can I find the definition of meancurv, gauscurv, foldind, curvind? I do not find it in the fswiki. Best, Feng___ 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] Calculate the cortical thickness in patients with brain tumor
Hi, Bruce Do you mean that if the tumor located in the subcortical area, there is not large impact to reconstruction; if the tumor located in the cortical regions, there will affect the cortex reconstruction? Another question is that I have MRI data from stroke patients. However, there are different lesions in the brain across the patients, including cerebral cortex and subcortical area. How could I perform reconstruction analysis? Best, Feng 发件人：Bruce Fischl 发送时间：2015-10-01 23:11 主题：Re: [Freesurfer] Calculate the cortical thickness in patients with brain tumor 收件人："Freesurfer support list" 抄送： Hi Feng it depends on where the tumor is cheers Bruce On Wed, 30 Sep 2015, chenhf_uestc wrote: > Hi, freesurfer experts, > > If my data came from the patients with brain tumors, could I perform > recon-all analyses to calculate cortical thickness, surface area and so on. > If not, could I mask the brain region with tumor and then conduct such > analyses? I think the tumor might lead to the inaccuracy of cortical > reconstruction > > Best, > Feng > > ___ 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] Question about the volume conversion in freesurfer
Yes, my data have been normalized to the MNI space. So, in my case, what should I do if I want to use the mri_surf2vol function? Best, Feng 发件人：Douglas Greve 发送时间：2015-09-29 00:00 主题：Re: [Freesurfer] Question about the volume conversion in freesurfer 收件人："freesurfer" 抄送： This is not an easy thing to do. First of all, did you apply a nonlinear registration to get the fMRI to the normalized MNI space? If so, then you can not do what you want with the data you have pre-processed. On 9/24/15 2:26 AM, chenhf_uestc wrote: Dear freesurfer experts, I want to compute functional connectivity based on the region with significantly different cortical thickness of two groups. The fMRI data have been preprocessed by using SPM software and normalized to the MNI space. However, I do not how to use the function mri_surf2vol. The required flagged arguments include --surfva, --hemi and --volreg (i.e., volume registration file). How can I set up the --volreg argument? What is the third arguments --volreg? The online manual states that contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. The format of this file is that as output by tkregister2 and includes the name of the subject. It will be assumed that the input surface values are sampled on the surface of this subject. Where could I find the volume registration file? Any help would be greatly appreciately. Best, Feng ___ 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] Calculate the cortical thickness in patients with brain tumor
Hi, freesurfer experts, If my data came from the patients with brain tumors, could I perform recon-all analyses to calculate cortical thickness, surface area and so on. If not, could I mask the brain region with tumor and then conduct such analyses? I think the tumor might lead to the inaccuracy of cortical reconstruction Best, Feng___ 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] Calculate the cortical thickness in patients with brain tumor
Hi, freesurfer experts, If my data came from the patients with brain tumors, could I perform recon-all analyses to calculate cortical thickness, surface area and so on. If not, could I mask the brain region with tumor and then conduct such analyses? I think the tumor might lead to the inaccuracy of cortical reconstruction Best, Feng___ 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] GRF correction in mri_glmfit-sim
I am also very interested in these questions, but I do not find the response. Could anyone provide the answers? Thanks, Feng 发件人："Meiling Li" 发送时间：2015-09-22 22:09 主题：[Freesurfer] GRF correction in mri_glmfit-sim 收件人："freesurfer-help" 抄送： Dear FS experts I do GRF correction using mri_glmfit-sim --grf in volume. I find --grf pos and --grf neg, but not --grf abs. My first question is, is the --grf just used for ONE-side correction? For instance, we can test, are the FCs of patients larger than that of healthy controls or smaller than the healthy controls? If I want to test the difference of FCs between patients and healthy controls, how do i do that? Please help me to check the following commands i used to do the TWO-sides correction (for example. voxel-wise p: 0.05, cluster-wise p: 0.05): mri_glmfit-sim --glmdir g2v0 --grf 1.3 pos --cwp .05 mri_glmfit-sim --glmdir g2v0 --grf 1.3 neg --cwp .05 Then i use the following commands to combine the 'pos' and 'neg' results together mri_convert grf.th1.3.neg.sig.cluster.mgh grf.th1.3.neg.sig.cluster.nii.gz mri_convert grf.th1.3.pos.sig.cluster.mgh grf.th1.3.pos.sig.cluster.nii.gz fslmaths grf.th1.3.pos.sig.cluster.nii.gz -add grf.th1.3.neg.sig.cluster.nii.gz grf.th1.3.sig.cluster.nii.gz Finally, i think the result grf.th1.3.sig.cluster.nii.gz is what i want, which is the difference between patients and healthy controls with GRF corrected, with vertex-wise p< 0.05 and cluster-wise p<0.05. Is it right? 2. The other question is, If i do the two-sides GRF correction(vertex-wise p<0.05 and cluster-wise p<0.05) with 'pos' or 'neg', should the vertex-wise or cluster-wise be 0.05/2 and 0.05/2? or 0.05 and 0.05? for example, we should write like this mri_glmfit-sim --glmdir g2v0 --grf -log10(0.05/2) pos --cwp 0.05/2 mri_glmfit-sim --glmdir g2v0 --grf -log10(0.05/2) neg --cwp 0.05/2 3. If i want to do cluster-based FDR correction, is there any FS command to do it? is it right if i load the statistic p map into MATLAB and do the FDR correction, then i use 'mri_volcluster --minsizevox' to threshold it to remove voxels smaller than the cluster size i set. Thank you very much for any help! All the best, Meiling___ 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] Question about the negative value of surface area
Dear Freesurfer experts,
I read the raw area file and the area resampled to the fsaverage space and
found several interesting things.
raw58l = read_curv('E:\fs_result\NC058\surf\lh.area'); % the range of the area
value is [-0.0471 6.2118]
raw58r = read_curv('E:\fs_result\NC058\surf\rh.area'); % the range of the area
value is [0 6.8963]
raw59l = read_curv('E:\fs_result\NC059\surf\lh.area'); % the range of the area
value is [-0.3347 5.4892]
raw59r = read_curv('E:\fs_result\NC059\surf\rh.area'); % the range of the area
value is [-1818 5.4269]
The first question, what is the unit of the area file in the surf folder (such
as lh.area), mm2? Why the minimal value of the area can be less than zero?
Subsequently, I perform further experiments, reading the resampled area file.
resamp_58l = load_mgh('E:\fs_result\NC058\surf\lh.area.fsaverage.mgh'); % the
range of the area value is [-0.0118 7.4073]
resamp_58r = load_mgh('E:\fs_result\NC058\surf\rh.area.fsaverage.mgh'); % the
range of the area value is [0 19.0191]
resamp_59l = load_mgh('E:\fs_result\NC059\surf\lh.area.fsaverage.mgh'); % the
range of the area value is [-0.3937 9.9084]
resamp_59r = load_mgh('E:\fs_result\NC059\surf\rh.area.fsaverage.mgh'); % the
range of the area value is -0.0909 8.2306[]
The second question, why the value of some area file change a lot? For example,
the maximum value of raw58r is 6.8963, but 19.0191 of resampled one.
Next,
resamp_smooth5_58l =
load_mgh('E:\fs_result\NC058\surf\lh.area.fwhm5.fsaverage.mgh'); % the range
of the area value is [0 1.7293]
resamp_smooth5_58r =
load_mgh('E:\fs_result\NC058\surf\rh.area.fwhm5.fsaverage.mgh'); % the range
of the area value is [0 2.1877]
resamp_smooth5_59l =
load_mgh('E:\fs_result\NC059\surf\lh.area.fwhm5.fsaverage.mgh'); % the range
of the area value is [0 1.2875]
resamp_smooth5_59r =
load_mgh('E:\fs_result\NC059\surf\rh.area.fwhm5.fsaverage.mgh'); % the range
of the area value is [0 1.3542]
The third question, why all the minimal values after smooth was zero? Why all
the maximal values after smooth reduce a lot?
Finally,
resamp_smooth25_58l =
load_mgh('E:\fs_result\NC058\surf\lh.area.fwhm25.fsaverage.mgh'); % the range
of the area value is [0 1.2014]
resamp_smooth25_58r =
load_mgh('E:\fs_result\NC058\surf\rh.area.fwhm25.fsaverage.mgh'); % the range
of the area value is [0 1.2611]
resamp_smooth25_59l =
load_mgh('E:\fs_result\NC059\surf\lh.area.fwhm25.fsaverage.mgh'); % the range
of the area value is [0 0.9730]
resamp_smooth25_59r =
load_mgh('E:\fs_result\NC059\surf\rh.area.fwhm25.fsaverage.mgh'); % the range
of the area value is [0 1.0119]
The final question, why all the maximal values of fwhm25 smooth are less than
the values of fwhm5 smooth?
How can I get the area value in the recon-all analyses? The cortical thickness
is the distance betwwen the white matter and the pial, but what is the
procedures the area value obtained? If there any reference? My freesurfer
version is stable v5.3.0.
Any help would be greatly appreciately!
Best,
Feng___
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] Questions about the files of lh.aparc.stats and lh.aparc.DKTatlas40.stats
Dear Freesurfer experts, In the stats folder of subject in the SUBJECTS_DIR, I found the files of lh.aparc.DKTatlas40.stats and lh.aparc.stats. Are there statistical results belong to two different atlas? Because the values and brain regions are different in these two files. In these two files, I found the command "mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab NC058 lh white" and "mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab NC058 lh white". So, the atlases are the lh.aparc.annot and lh.aparc.DKTatlas40.stats, respectively. Right? However, when I open these two atlas (attached aparc.annot.ctab and aparc.annot.DKTatlas40.ctab), I found the contents are same. In addition, I would really want to know that the value in the aparc.annot.ctab. For ex. 1 bankssts 25 100 400; what does the values mean? 25 100 40 0 Best, Feng lh.aparc.stats Description: Binary data lh.aparc.DKTatlas40.stats Description: Binary data aparc.annot.ctab Description: Binary data aparc.annot.DKTatlas40.ctab Description: Binary data ___ 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] Question about the volume conversion in freesurfer
Yes, my data have been normalized to the MNI space. So, in my case, what should I do if I want to use the mri_surf2vol function? Best, Feng 发件人：Douglas Greve 发送时间：2015-09-29 00:00 主题：Re: [Freesurfer] Question about the volume conversion in freesurfer 收件人："freesurfer" 抄送： This is not an easy thing to do. First of all, did you apply a nonlinear registration to get the fMRI to the normalized MNI space? If so, then you can not do what you want with the data you have pre-processed. On 9/24/15 2:26 AM, chenhf_uestc wrote: Dear freesurfer experts, I want to compute functional connectivity based on the region with significantly different cortical thickness of two groups. The fMRI data have been preprocessed by using SPM software and normalized to the MNI space. However, I do not how to use the function mri_surf2vol. The required flagged arguments include --surfva, --hemi and --volreg (i.e., volume registration file). How can I set up the --volreg argument? What is the third arguments --volreg? The online manual states that contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. The format of this file is that as output by tkregister2 and includes the name of the subject. It will be assumed that the input surface values are sampled on the surface of this subject. Where could I find the volume registration file? Any help would be greatly appreciately. Best, Feng ___ 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] The range of value of the area file
Dear Freesurfer experts,
I read the raw area file and the area resampled to the fsaverage space and
found several interesting things.
raw58l = read_curv('E:\fs_result\NC058\surf\lh.area'); % the range of the area
value is [-0.0471 6.2118]
raw58r = read_curv('E:\fs_result\NC058\surf\rh.area'); % the range of the area
value is [0 6.8963]
raw59l = read_curv('E:\fs_result\NC059\surf\lh.area'); % the range of the area
value is [-0.3347 5.4892]
raw59r = read_curv('E:\fs_result\NC059\surf\rh.area'); % the range of the area
value is [-1818 5.4269]
The first question, what is the unit of the area file in the surf folder (such
as lh.area), mm2? Why the minimal value of the area can be less than zero?
Subsequently, I perform further experiments, reading the resampled area file.
resamp_58l = load_mgh('E:\fs_result\NC058\surf\lh.area.fsaverage.mgh'); % the
range of the area value is [-0.0118 7.4073]
resamp_58r = load_mgh('E:\fs_result\NC058\surf\rh.area.fsaverage.mgh'); % the
range of the area value is [0 19.0191]
resamp_59l = load_mgh('E:\fs_result\NC059\surf\lh.area.fsaverage.mgh'); % the
range of the area value is [-0.3937 9.9084]
resamp_59r = load_mgh('E:\fs_result\NC059\surf\rh.area.fsaverage.mgh'); % the
range of the area value is -0.0909 8.2306[]
The second question, why the value of some area file change a lot? For example,
the maximum value of raw58r is 6.8963, but 19.0191 of resampled one.
Next,
resamp_smooth5_58l =
load_mgh('E:\fs_result\NC058\surf\lh.area.fwhm5.fsaverage.mgh'); % the range
of the area value is [0 1.7293]
resamp_smooth5_58r =
load_mgh('E:\fs_result\NC058\surf\rh.area.fwhm5.fsaverage.mgh'); % the range
of the area value is [0 2.1877]
resamp_smooth5_59l =
load_mgh('E:\fs_result\NC059\surf\lh.area.fwhm5.fsaverage.mgh'); % the range
of the area value is [0 1.2875]
resamp_smooth5_59r =
load_mgh('E:\fs_result\NC059\surf\rh.area.fwhm5.fsaverage.mgh'); % the range
of the area value is [0 1.3542]
The third question, why all the minimal values after smooth was zero? Why all
the maximal values after smooth reduce a lot?
Finally,
resamp_smooth25_58l =
load_mgh('E:\fs_result\NC058\surf\lh.area.fwhm25.fsaverage.mgh'); % the range
of the area value is [0 1.2014]
resamp_smooth25_58r =
load_mgh('E:\fs_result\NC058\surf\rh.area.fwhm25.fsaverage.mgh'); % the range
of the area value is [0 1.2611]
resamp_smooth25_59l =
load_mgh('E:\fs_result\NC059\surf\lh.area.fwhm25.fsaverage.mgh'); % the range
of the area value is [0 0.9730]
resamp_smooth25_59r =
load_mgh('E:\fs_result\NC059\surf\rh.area.fwhm25.fsaverage.mgh'); % the range
of the area value is [0 1.0119]
The final question, why all the maximal values of fwhm25 smooth are less than
the values of fwhm5 smooth?
How can I get the area value in the recon-all analyses? The cortical thickness
is the distance betwwen the white matter and the pial, but what is the
procedures the area value obtained?
Any help would be greatly appreciately!
Best,
Feng___
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] .mgh file not load into surfstats
Hi, Myriam Actually, you do not need to convert a .mgh file to a .obj file, just use the SurfStatReadData function rather than SurfStatReadSurf. In addition, you can use load_mgh or MRIread function (Matlab function) in Freesurfer to read the mgh file. For the error "using + Matrix dimensions must agree", I guess that the recon-all analyses were conducted in the subject native space, and the number of vertices in left/right hemi is different. You should first resample your data to the standard space (here, it's fsaverage space). Hope these helps. Best, Feng 发件人：Myriam Oliver 发送时间：2015-09-25 20:46 主题：Re: [Freesurfer] .mgh file not load into surfstats 收件人："Freesurfer support list" 抄送： Hi Bruce! Thank you for your response. Sorry about the incomplete information, I need the average surface of each participant, so for me it will be great to use the output already generated for freesurfer. However, it is not read by surfstats. So, one solution was to change to .mgh format to .obj The solution two can be use the lh.white which surfstats reads and change the matrix dimensions so I can compare all subjects. This is the command I use for each subject to change the matrix dimensions: mri_surf2surf --s ' subjectid ' --hemi lh --sval-tal-xyz white --tval talairach.white --tval-xyz --trgsubject ' subjectid %Average surface left_files = SurfStatListDir([cd filesep 'lh.white.transform'], []); right_files = SurfStatListDir([cd filesep 'rh.white.transform'], []); f = [left_files, right_files]; avsurf = SurfStatAvSurf(f); The error is: Error using + Matrix dimensions must agree. Error in SurfStatAvSurf (line 36) surf.coord=fun(surf.coord,double(s.coord)); Thank you! 2015-09-24 15:50 GMT-04:00 Bruce Fischl : when you say "it does not work either', what do you mean? Please remember to send us the entire screen output of commands you are asking about On Thu, 24 Sep 2015, Myriam Oliver wrote: > Dear Freesurfers, > > I wanted to ask you if you know how can I convert a .mgh file to a .obj > file. > > I want to run surfstats (specifically SurfStatReadSurf ) but it does not > read .mgh files (i.e, the surface file; lh.w-g.pct.mgh.fsaverage.mgh). > Although, it reads the lh.white, but I need the average, as otherwise I have > an error of matrix dimension between subjects. > > I try using the lh.white and changing the matrix dimensions through: > mri_surf2surf --s ' subjectid ' --hemi lh --sval-tal-xyz white --tval > talairach.white --tval-xyz --trgsubject ' subjectid > > But it does not work either. > > Any help about how can I use the .mgh file in surfstats? > > Thanks! > > ___ 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. -- Myriam___ 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] Query about the fsgd file and glm model in freesurfer
Dear freesurfer experts, I have some questions about the statistical model in freesurfer. In my experiments, I would like to compare the cortical thickness of two groups (schizophrenia patients and healthy controls) with age and sex as covariates. I want to know that the variable in fsgd file must be continuous covariate? Could the fsgd file like this (attached fsgd1.png): There are two classes and two columns of age and sex variables in the fsgd file. Now, there are six regressors. Regressor 1: ones for subjects in Group SCH, 0 otherwise; Regressor 2: ones for subjects in Group HC, 0 otherwise; Regressor 3: age for subjects in Group SCH , 0 otherwise; Regressor 4: age for subjects in Group HC, 0 otherwise. Regressor 5: sex for subjects in Group SCH, 0 otherwise. Regressor 6: sex for subjects in Group HC, 0 otherwise. If I want to compare the cortical thickness of two groups and regress out the effect of age and sex, the contrast is 1 -1 0 0 0 0. Or I must put it in this way (attached fsgd2.png): There are four classes and one column of age variable in the fsgd file. Now, there are eight regressors. Regressor 1: ones for SCHmale subjects, 0 otherwise. Regressor 2: ones for SCHfemale subjects, 0 otherwise. Regressor 3: ones for HCmale subjects, 0 otherwise. Regressor 4: ones for HCfemale subjects, 0 otherwise. Regressor 5: age for SCHmale subjects, 0 otherwise. Regressor 6: age for SCHfemale subjects, 0 otherwise. Regressor 7: age for HCmale subjects, 0 otherwise. Regressor 8: age for HCfemale subjects, 0 otherwise. If I want to compare the cortical thickness of two groups and regress out the effect of age and sex, the contrast is 0.5 0.5 -0.5 -0.5 0 0 0 0. Which one is right, or both of them are right? If just the latter is right, what is the rationale behind this? Why treat continuous and discrete variables differently here. In the general linear model Y = XB+U, X is a matrix that might be a design matrix, B is a matrix containing parameters and U is a matrix containing errors or noise. Why we cannot treat the age and sex equally in the GLM of freesurfer software? All the best, Feng___ 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] Question about the volume conversion in freesurfer
Dear freesurfer experts, I want to compute functional connectivity based on the region with significantly different cortical thickness of two groups. The fMRI data have been preprocessed by using SPM software and normalized to the MNI space. However, I do not how to use the function mri_surf2vol. The required flagged arguments include --surfva, --hemi and --volreg (i.e., volume registration file). How can I set up the --volreg argument? What is the third arguments --volreg? The online manual states that contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. The format of this file is that as output by tkregister2 and includes the name of the subject. It will be assumed that the input surface values are sampled on the surface of this subject. Where could I find the volume registration file? Any help would be greatly appreciately. Best, Feng___ 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] Question about the multiple comparison correction in FreeSurfer
Hi, Douglas
Thanks for your reply. I have two further questions here. First, I know that
--grf is gaussian random fields for the volume (not surface). Could the Monte
Carlo simulation such as "--cache 4 neg" be used for correction on volume?
Because the manual introduces this method for the correction on surface, and
thus I do not whether this method could be used on volume.
Second, in the Monte Carlo simulation on surface "--cache 4 neg", I can
specify the sign (neg for negative, pos, or abs). However, in the grf
correction, there are "--grf 3 pos or neg ". Could I specify the sign "abs"
such as "--grf 3 abs".
Best,
Feng
发件人：Douglas N Greve
发送时间：2015-09-22 05:35
主题：Re: [Freesurfer] Question about the multiple comparison correction in
FreeSurfer
收件人："freesurfer"
抄送：
--grf is gaussian random fields for the volume (not surface).
Re: --2spaces, your understanding is correct.
FDR: you can do it in matlab, something like
sig = MRIread('sig.mgh');
p = 10.^-abs(sig.vol)
pthresh = fast_fdrthresh(p,fdr);
ind = find(p < pthresh);
sig.vol(ind) = 0;
MRIwrite(sig,'sig.fdr.mgh')
It is also possible with mri_surfcluster
On 09/20/2015 12:47 PM, chenhf_uestc wrote:
> Dear Freesurfer experts,
> I have some questions about the multiple comparison correction method
> for group analysis in Freesurfer. The manual stated that we could use
> the commands as follows:
> mri_glmfit-sim \
>--glmdir lh.gender_age.glmdir \
>--cache 4 neg \
>--cwp 0.05\
>--2spaces
> This is the alphasim correction, right? When I write this command in
> terminal, there are detailed explanations about this command. In the
> above-mentioned command, I used parameter "--cache threshold sign". In
> this way, a precomputed Z Monte Carlo simulation (--cache) was used.
> Also, I can run my own simulation by using "--sim mc-z
> iterations threshold".
> However, I find an interesting parameter "--grf threshold sign". I
> would like to know whether this parameter could give me another
> correction method rather than alphasim, i.e. the gaussian random field
> correction method? In other words, if I add the parameter "grf", then
> the mri_glmfit-sim performs the GRF correction; if I do not add this
> parameter, then mri_glmfit-sim performs alphasim correction, right?
> Another question is about the parameter "--2spaces: adjust p-values
> for two hemispheres", I give an example here. I want to perform
> cluster-level correction of *p<0.05* based on vertex-wise thershold of
> 4 (p < .0001) for the left hemisphere; and perform the same correction
> for the right hemisphere. So, I should add the parameter "--2spaces".
> Is this equal to perform cluster-level correction of *p<0.025 (0.05/2,
> if I also want to examine the subcortical diferences, then the cluster
> p value should be 0.05/3)* based on vertex-wise thershold of 4 (p <
> .0001). Have I understood correctly?
> The third question is that could I perform False discovery rate (FDR)
> using commands rather than GUI? If not, could I load the sig.mgh file
> into MatLab and then perform FDR correction manually?
> In addition to the aforementioned multiple comparison correction
> method, is there other correction method in Freesurfer?
> Best,
> Feng
>
>
> ___
> 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/
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add
[Freesurfer] How could I display the tksurfer correctly
Dear Freesurfer experts, I use Oracle VM VirtualBox to run Freesurfer software and I want to perform FDR correction in TKSurfer. However, I cannot get the whole window size (attached 1.png), and thus I cannot find the FDR option. Actually, there are lots of options (2.png) cannot be displayed in 1.png. I try to change the window resolution, but I failed because now is the max resolution. Could anyone give me some suggestions? Best, Feng___ 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] Question about the multiple comparison correction in FreeSurfer
Dear Freesurfer experts, I have some questions about the multiple comparison correction method for group analysis in Freesurfer. The manual stated that we could use the commands as follows: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces This is the alphasim correction, right? When I write this command in terminal, there are detailed explanations about this command. In the above-mentioned command, I used parameter "--cache threshold sign". In this way, a precomputed Z Monte Carlo simulation (--cache) was used. Also, I can run my own simulation by using "--sim mc-z iterations threshold". However, I find an interesting parameter "--grf threshold sign". I would like to know whether this parameter could give me another correction method rather than alphasim, i.e. the gaussian random field correction method? In other words, if I add the parameter "grf", then the mri_glmfit-sim performs the GRF correction; if I do not add this parameter, then mri_glmfit-sim performs alphasim correction, right? Another question is about the parameter "--2spaces : adjust p-values for two hemispheres", I give an example here. I want to perform cluster-level correction of p<0.05 based on vertex-wise thershold of 4 (p < .0001) for the left hemisphere; and perform the same correction for the right hemisphere. So, I should add the parameter "--2spaces". Is this equal to perform cluster-level correction of p<0.025 (0.05/2, if I also want to examine the subcortical diferences, then the cluster p value should be 0.05/3) based on vertex-wise thershold of 4 (p < .0001). Have I understood correctly? The third question is that could I perform False discovery rate (FDR) using commands rather than GUI? If not, could I load the sig.mgh file into MatLab and then perform FDR correction manually? In addition to the aforementioned multiple comparison correction method, is there other correction method in Freesurfer? Best, Feng___ 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] Can MRIread function read .mgz file
Hi, Bruce
I may find the reason. Actually, I can load the file into freeview. My
colleagure can read this file using MRIread on Linux system but I failed using
the Windows system. In the MRIread function, there are ' unix(sprintf('zcat %s
> %s', fname, new_fname)) ;' and 'unix(sprintf('rm %s', fname))'. I think they
cannot run on the Windows system. Is this the reason? If so, how can I solve it
or I must use this function on the Linux system to read .mgz file.
Best,
Feng
发件人：Bruce Fischl
发送时间：2015-09-17 22:59
主题：Re: [Freesurfer] Can MRIread function read .mgz file
收件人："Freesurfer support list"
抄送：
Hi Feng
can you load that file into tksurfer/freeview? It sounds like something
is wrong with it. You should also just run ls -l on it and see if it looks
reasonable in terms of size and permissions
cheers
Bruce
On Thu, 17 Sep 2015, chenhf_uestc wrote:
> Dear Freesurfer expert,
>
> How could I read the .mgz file into Matlab, the online manual FAQ stated
>
> Q. Can I load FreeSurfer output in Matlab?
>
> A: If you write it as .mgz format then load_mgh (or MRIread) will read it.
>
> In addition, in the MRIread function, it stated that
>
> % mri = MRIread(fstring,headeronly)
> %
> % Reads in a volume based on the fstring. fstring can be:
> % 1. A stem, in which case the format and full file name is determined
> % by finding a file on disk called fstring.ext, where ext can be
> % either mgh, mgz, img, bhdr, nii, or nii.gz
> % 2. MGH file. Eg, f.mgh or f.mgz
>
> However, I cannot read the .mgz file using MRIread
>
> A = mriread('lh.thickness.20.mgz');
> ??? SWITCH expression must be a scalar or string constant.
>
> Error in ==> load_mgh at 158
> switch type
>
> Error in ==> MRIread at 87
> [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
>
> If this function cannot read the .mgz file, how can I read it?
>
> Best,
> Feng
>
>
> 2015-09-17
>
>
> chenhf_uestc
>
>
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[Freesurfer] Can MRIread function read .mgz file
Dear Freesurfer expert,
How could I read the .mgz file into Matlab, the online manual FAQ stated
Q. Can I load FreeSurfer output in Matlab?
A: If you write it as .mgz format then load_mgh (or MRIread) will read it.
In addition, in the MRIread function, it stated that
% mri = MRIread(fstring,headeronly)
%
% Reads in a volume based on the fstring. fstring can be:
% 1. A stem, in which case the format and full file name is determined
% by finding a file on disk called fstring.ext, where ext can be
% either mgh, mgz, img, bhdr, nii, or nii.gz
% 2. MGH file. Eg, f.mgh or f.mgz
However, I cannot read the .mgz file using MRIread
A = mriread('lh.thickness.20.mgz');
??? SWITCH expression must be a scalar or string constant.
Error in ==> load_mgh at 158
switch type
Error in ==> MRIread at 87
[mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly);
If this function cannot read the .mgz file, how can I read it?
Best,
Feng
2015-09-17
chenhf_uestc ___
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[Freesurfer] Question about the raw thickness range
Dear Freesurfer experts, I have two question about my freesurfer results. 1. I performed recon-all analyses on my data and found all the data's maximal value of cortical thickness is 5. Is there any standardization procedure in the recon-all that normalize the maximum value to 5? In addition, is there any lower bound (non-zero value) for cortical thickness 2. Before group analysis, I run the recon-all subject -qcache and generate the resampled and smoothed data. The online manual stated "When you have run recon-all with the -qcache option, recon-all will resample data onto the average subject (fsaverage) and smooth it at various FWHM (full-width/half-max), usually 0, 5, 10, 10, 20, and 25mm. This can speed later processing. The data for this tutorial have been cached, so run: mris_preproc --fsgd gender_age.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.gender_age.thickness.10.mgh Since I have resampled the data to fsaverage by using -qcache option, what is the function of the option --target fsaverage ? resample again? If so, could I remove the option --target fsaverage in the mris_preproc? Best, Feng___ 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] Questions about the correction methods in Surfstat
Dear Surfstat Users, I have a question about the RFT correction method in the Surfstat(http://www.math.mcgill.ca/keith/surfstat/). In the online manual, the command to perform RFT correction is as follows: [ pval, peak, clus ] = SurfStatP( slm, mask ); pval.P contains P-values for peaks, and pval.C contains P-values for clusters. This special structure is recognised by SurfStatView which draws the figure in a special way: SurfStatView( pval, avsurf, 'Males-females removing age' ); The output figure is attached. In the colorbar of the figure, left represents cluster corrected p value and right one represents the vertex corrected p value, right? So, the warm color region in the figure can be survived by the RFT vertex correction, and the cool color region in the figure can be survived by the RFT cluster correction, right? If so, the regions with either warm or cool color region that can be survived after correction. When I report the results, I can report the regions with warm color (vertex level correction) or report the regions with cool color (cluster level correction), right? In addtion, how can I understand the region overlapped by the warm and cool color (like he postier cingulate cortex), can simultaneously pass double correction of vertex level and cluster level? The final question is about the RFT cluster correction method, in the SPM or other software (like REST). Generally, on the cluster level correction, you should be based on a voxel (vertex) uncorrected height threshold of e.g. p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05, right? What is the detailed correction procedure in the Surfstat software? Any help would be greatly appreciate. Best, Feng___ 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] Query about transformations in the recon-all
Hi, Bruce Thanks for your reply. Another question is What is talairach transformation procedure (This computes the affine transform from the orig volume to the MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script called talairach). Why I need to transform from native space to MNI305 (We perform recon-all in the native space)? Best, Feng 发件人：Bruce Fischl 发送时间：2015-08-18 22:09 主题：Re: [Freesurfer] Query about transformations in the recon-all 收件人："Freesurfer support list" 抄送： Hi Feng we compute many transforms for many reasons. The em reg is computed once in the image with skull to help with skull stripping, then again to the GCA atlas to initialize the nonlinear transform for computing the aseg segmentation. cheers Bruce On Tue, 18 Aug 2015, chenhf_uestc wrote: > Dear Freesurfer experts, > > I have some questions in the recon-all. After reading online manual and > discussing with the experts in > the maillist, I have known all the recon-all procedures performed in the > individual native space. > However, I very confuse that there are many transformations in the recon-all, > e.g., 1. talairach > transformation (This computes the affine transform from the orig volume to > the MNI305 atlas using the > MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script > called talairach), why I > need transform from native space to MNI305; 2. EM (GCA) Registration > (Computes transform to align the > mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/average). > What is the GCA atlas? > what is the usage of this atlas? 3. CA Register (Computes a nonlinear > transform to align with GCA > atlas. Creates the file mri/transform/talairach.m3z). Why we should align > with GCA atlas? This > transform is nonlinear, and what is the transform in the EM (GCA) > Registration (Affine? 12 dof?); 4. > EM Registration, with Skull (Computes transform to align volume > mri/nu_noneck.mgz with GCA volume > possessing the skull); > > Is there any detailed documentation in the online manual to introduce these > transformation? Could > anyone give me a website? > > Any help would be greatly appreciate. > > Best, > Feng > > > ___ 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] Query about transformations in the recon-all
Dear Freesurfer experts, I have some questions in the recon-all. After reading online manual and discussing with the experts in the maillist, I have known all the recon-all procedures performed in the individual native space. However, I very confuse that there are many transformations in the recon-all, e.g., 1. talairach transformation (This computes the affine transform from the orig volume to the MNI305 atlas using the MINC program mritotal (see Collins, et al, 1994) through a FreeSurfer script called talairach), why I need transform from native space to MNI305; 2. EM (GCA) Registration (Computes transform to align the mri/nu.mgz volume to the default GCA atlas found in FREESURFER_HOME/average). What is the GCA atlas? what is the usage of this atlas? 3. CA Register (Computes a nonlinear transform to align with GCA atlas. Creates the file mri/transform/talairach.m3z). Why we should align with GCA atlas? This transform is nonlinear, and what is the transform in the EM (GCA) Registration (Affine? 12 dof?); 4. EM Registration, with Skull (Computes transform to align volume mri/nu_noneck.mgz with GCA volume possessing the skull); Is there any detailed documentation in the online manual to introduce these transformation? Could anyone give me a website? Any help would be greatly appreciate. Best, Feng___ 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] Is the fsaverage in the MNI space?
Dear freesurfer experts, The freesurfer online manual stated that before group analysis, we should resample data onto the common space (fsaverage). I have three questions here. First, Is the fsaverage file in the MNI space? In some previous studies, they report significant clusters with MNI coordinates. So, I would like to know whether this "common space" is equal to MNI space. Second, what does resample mean? Normalization--register the surf data to the fsaverage space? In my experience, I just used resample to change the voxel size in the volume data (e.g., before 1*1*1, after 3*3*3). The final question is that the fsaverage file is generated from my data or just a prior template? Thanks in advance. Best, Feng ___ 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] Question about the outputs of recon-all
Hi, Douglas Thanks for your reply. So, as you stated, the fsaverage is already in the MNI space? Because my fMRI data are in the MNI space (after normalization) and I want to extract the region with significant different cortical thickness as seed to calculate functional connectivity. Best, Feng 发件人：Douglas N Greve 发送时间：2015-08-12 22:39 主题：Re: [Freesurfer] Question about the outputs of recon-all 收件人："freesurfer" 抄送： fsaverage is the surface-based common-space analogous to talairach for MNI space. This is the space where group analysis is done on the surface. You can run mris_preproc to get a stack of data in fsaverage space prior to running group analysis with mri_glmfit. See the on-line tutorials on the wiki. On 08/11/2015 09:46 PM, chenhf_uestc wrote: > Dear Freesurfer experts, > I am a new user of freesurfer and I just performed recon-all analyses. > I have some questions about the pipeline (may be very simple ^_^). > In the fMRI, I used SPM8 toolkit to perform preprocessing. After > normalization, the images were transform to the MNI space. In the > freesurfer, there are many folders in the output subject dir, e.g., > bem, mri, script, surf. The first question, were the recon-all > analyses performed in the individual spave (I mean, unlike spm or > other software, there is no normalization procedure in freesurfer)? > If in the individual space, we should transform all subjects' files > into a common space for group-level analysis. How can I transform > them? Did I transfrom these into MNI space or other space? In the > fswiki, I have known that there is a fsaverage space. So, the second > question is that what is the fsaverage space and what is the aim to > introduce such space. Can I regard fsaverage space as a intermediate > between individual space and MNI space? Further, in the recon-all > analysis, there is a procedure of talairach transformation. Were the > outputs transformed into talairach space? > Any help will be greatly appreciately! > Best, > Feng > > > ___ > 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 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] Question about the outputs of recon-all
Dear Freesurfer experts, I am a new user of freesurfer and I just performed recon-all analyses. I have some questions about the pipeline (may be very simple ^_^). In the fMRI, I used SPM8 toolkit to perform preprocessing. After normalization, the images were transform to the MNI space. In the freesurfer, there are many folders in the output subject dir, e.g., bem, mri, script, surf. The first question, were the recon-all analyses performed in the individual spave (I mean, unlike spm or other software, there is no normalization procedure in freesurfer)? If in the individual space, we should transform all subjects' files into a common space for group-level analysis. How can I transform them? Did I transfrom these into MNI space or other space? In the fswiki, I have known that there is a fsaverage space. So, the second question is that what is the fsaverage space and what is the aim to introduce such space. Can I regard fsaverage space as a intermediate between individual space and MNI space? Further, in the recon-all analysis, there is a procedure of talairach transformation. Were the outputs transformed into talairach space? Any help will be greatly appreciately! Best, Feng___ 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] freesurfer problem report
Hi Zeke, When I enter the commands $> cd /media/sf_E_DRIVE/output/nv001/mri $> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz The output is in the attached file 1.txt. However, if I keep the subjects_dir (/usr/local/freesurfer/subjects) as default, there is no error information (attached file 2. log). The attached file 3.log is the file I changed the subjects_dir to /media/sf_E_DRIVE/output. This problem confused me several days. I also used other computers (install VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G ) and came across the same problem. If you need further information, please do not hesitate to contact me. Best, Feng 发件人：zkauf...@nmr.mgh.harvard.edu 发送时间：2015-06-15 04:58 主题：Re: [Freesurfer] freesurfer problem report 收件人："Freesurfer support list" 抄送： Hello Feng Liu, What is the terminal output when you enter the following commands: $> cd /media/sf_E_DRIVE/output/nv001/mri $> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz -Zeke > Dear freesurfer experts, > > I came across a problem when I run freesurfer. I just download the > freesurfer software ( VirtualboxXubuntu 12.04stable v5.3.015 Aug > 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G > ). I install the software and configuration, and I changed subjects_dir as > /media/sf_E_DRIVE. When I executed the command recon-all -s nv001 -all, > there is error in the command window. > > The information of freesurfer problem are as follows: > FREESURFER_HOME: /usr/local/freesurfer > > Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 > > Debian version: wheezy/sid > > Kernel info: Linux 3.2.0-23-generic i686 > > - > Please include the following additional information in your report: > > 1) subject name > nv001 > 2) the entire command-line executed > recon-all -s nv001 -all > 3) the error message generated > INFO: extension is mgz > # > #@# Talairach Sun Jun 14 12:25:31 EDT 2015 > /media/sf_E_DRIVE/output/nv001/mri > > mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz > > Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 > 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux > > recon-all -s nv001 -all exited with ERRORS at Sun Jun 14 12:25:42 EDT > 2015 > > For more details, see the log file > /media/sf_E_DRIVE/output/nv001/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > 4) optionally include the subject's /script/recon-all.log > Attached > > However, if I am not change the subjects_dir (usr the default: > /usr/local/freesurfer/subjects), there is no error information. > > I do not know where I am wrong. > Would greatly appreciate any form of help! > > 2015-06-15 > > > > Feng Liu, Ph.D. > Department of Radiology, > Tianjin Medical University General Hospital, > No. 154, Anshan Road, Heping District, Tianjin > 300052.___ > 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. file 1.txt Description: Binary data file 2.log Description: Binary data file 3.log Description: Binary data ___ 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] freesurfer problem report
Dear freesurfer experts, I came across a problem when I run freesurfer. I just download the freesurfer software ( VirtualboxXubuntu 12.04stable v5.3.015 Aug 2013freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz9.0G ). I install the software and configuration, and I changed subjects_dir as /media/sf_E_DRIVE. When I executed the command recon-all -s nv001 -all, there is error in the command window. The information of freesurfer problem are as follows: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-23-generic i686 - Please include the following additional information in your report: 1) subject name nv001 2) the entire command-line executed recon-all -s nv001 -all 3) the error message generated INFO: extension is mgz # #@# Talairach Sun Jun 14 12:25:31 EDT 2015 /media/sf_E_DRIVE/output/nv001/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux recon-all -s nv001 -all exited with ERRORS at Sun Jun 14 12:25:42 EDT 2015 For more details, see the log file /media/sf_E_DRIVE/output/nv001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 4) optionally include the subject's /script/recon-all.log Attached However, if I am not change the subjects_dir (usr the default: /usr/local/freesurfer/subjects), there is no error information. I do not know where I am wrong. Would greatly appreciate any form of help! 2015-06-15 Feng Liu, Ph.D. Department of Radiology, Tianjin Medical University General Hospital, No. 154, Anshan Road, Heping District, Tianjin 300052. recon-all.log Description: Binary data ___ 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.
