Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20
charujing123
I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order
On 6/20/14 4:27 AM, charujing123 wrote:
Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20
charujing123
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi doug, Thanks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha
2014-06-20
charujing123
发件人：Douglas Greve greve@nmr.mgh.harvard.edu 发送时间：2014-06-20 16:51 主题：Re: [Freesurfer] some questions about optseq 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order
On 6/20/14 4:27 AM, charujing123 wrote:
Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20
charujing123
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I don't think there is anything wrong with what you have. Is there a problem? You could shorten it to something like 240sec or so.
On 6/20/14 1:43 PM, charujing123 wrote:
Hi doug, Th?anks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha 2014-06-20
charujing123
*? ??:*Douglas Greve greve@nmr.mgh.harvard.edu *? ???:*2014-06-20 16:51 *? ?:*Re: [Freesurfer] some questions about optseq *? ??:*"freesurfer"freesurfer@nmr.mgh.harvard.edu *? ?:*
I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order
On 6/20/14 4:27 AM, charujing123 wrote:
Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20
charujing123
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
Hi doug, Thanks doug. Here are two questions that I am not sure: 1, Each stimulus condition has three elements, i.e. cue fixation and picture. However it is only picture element that will be analyzed. The time window of picture will not influence the efficiency of sequence? 2, After stimulus presented(last 1.5s), subjects will response to the picture in the specific time window. This time window followed the stimulus, and it varied from 2.5s to ~8.5s. However, some trials was not followed by NULL trial. That is to say, there is no time to response after some trials. Thanks All the best Rujing Zha
2014-06-20
charujing123
发件人：Douglas Greve greve@nmr.mgh.harvard.edu 发送时间：2014-06-20 21:18 主题：Re: [Freesurfer] some questions about optseq 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
I don't think there is anything wrong with what you have. Is there a problem? You could shorten it to something like 240sec or so.
On 6/20/14 1:43 PM, charujing123 wrote:
Hi doug, Thanks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha
2014-06-20
charujing123
发 件人：Douglas Greve greve@nmr.mgh.harvard.edu 发 送时间：2014-06-20 16:51 主 题：Re: [Freesurfer] some questions about optseq 收 件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄 送：
I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order
On 6/20/14 4:27 AM, charujing123 wrote:
Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20
charujing123
_______________________________________________ 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
On 6/20/14 4:14 PM, charujing123 wrote:
Hi doug, Thanks doug. Here are two questions that I am not sure: 1, Each stimulus condition has three elements, i.e. cue fixation and picture. However it is only picture element that will be analyzed. The time window of picture will not influence the efficiency of sequence?
Not much
2, After stimulus presented(last 1.5s), subjects will response to the picture in the specific time window. This time window followed the stimulus, and it varied from 2.5s to ~8.5s. However, some trials was not followed by NULL trial. That is to say, there is no time to response after some trials.
You can create a minimum fixed amount of after the trial with --tnullmin doug
Thanks All the best Rujing Zha 2014-06-20
charujing123
*? ??:*Douglas Greve greve@nmr.mgh.harvard.edu *? ???:*2014-06-20 21:18 *? ?:*Re: [Freesurfer] some questions about optseq *? ??:*"freesurfer"freesurfer@nmr.mgh.harvard.edu *? ?:*
I don't think there is anything wrong with what you have. Is there a problem? You could shorten it to something like 240sec or so.
On 6/20/14 1:43 PM, charujing123 wrote:
Hi doug, Th?anks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha 2014-06-20
charujing123
*? ??:*Douglas Greve greve@nmr.mgh.harvard.edu *? ???:*2014-06-20 16:51 *? ?:*Re: [Freesurfer] some questions about optseq *? ??:*"freesurfer"freesurfer@nmr.mgh.harvard.edu *? ?:*
I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order
On 6/20/14 4:27 AM, charujing123 wrote:
Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20
charujing123
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
Hi doug Thanks very much. I see. When I add --tnullmin 2 --tnullmax 8, result looks weird. ======================================= [psylab16@centos1 ~]$ cat ex1-001.par 0.0000 2 2.000 1.0000 ev2 2.0000 0 2.000 1.0000 NULL 4.0000 1 2.000 1.0000 ev1 6.0000 0 2.000 1.0000 NULL 8.0000 1 2.000 1.0000 ev1 10.0000 0 2.000 1.0000 NULL 12.0000 1 2.000 1.0000 ev1 14.0000 0 2.000 1.0000 NULL 16.0000 1 2.000 1.0000 ev1 18.0000 0 2.000 1.0000 NULL 20.0000 2 2.000 1.0000 ev2 22.0000 0 2.000 1.0000 NULL 24.0000 1 2.000 1.0000 ev1 26.0000 0 2.000 1.0000 NULL 28.0000 1 2.000 1.0000 ev1 30.0000 0 2.000 1.0000 NULL 32.0000 2 2.000 1.0000 ev2 34.0000 0 2.000 1.0000 NULL 36.0000 2 2.000 1.0000 ev2 38.0000 0 2.000 1.0000 NULL 40.0000 2 2.000 1.0000 ev2 42.0000 0 2.000 1.0000 NULL 44.0000 2 2.000 1.0000 ev2 46.0000 0 2.000 1.0000 NULL 48.0000 1 2.000 1.0000 ev1 50.0000 0 2.000 1.0000 NULL 52.0000 2 2.000 1.0000 ev2 54.0000 0 2.000 1.0000 NULL 56.0000 1 2.000 1.0000 ev1 58.0000 0 2.000 1.0000 NULL 60.0000 2 2.000 1.0000 ev2 62.0000 0 2.000 1.0000 NULL 64.0000 2 2.000 1.0000 ev2 66.0000 0 2.000 1.0000 NULL 68.0000 1 2.000 1.0000 ev1 70.0000 0 2.000 1.0000 NULL 72.0000 1 2.000 1.0000 ev1 74.0000 0 2.000 1.0000 NULL 76.0000 1 2.000 1.0000 ev1 78.0000 0 2.000 1.0000 NULL 80.0000 2 2.000 1.0000 ev2 82.0000 0 2.000 1.0000 NULL 84.0000 2 2.000 1.0000 ev2 86.0000 0 2.000 1.0000 NULL 88.0000 2 2.000 1.0000 ev2 90.0000 0 2.000 1.0000 NULL 92.0000 1 2.000 1.0000 ev1 94.0000 0 2.000 1.0000 NULL 96.0000 1 2.000 1.0000 ev1 98.0000 0 2.000 1.0000 NULL 100.0000 1 2.000 1.0000 ev1 102.0000 0 2.000 1.0000 NULL 104.0000 2 2.000 1.0000 ev2 106.0000 0 2.000 1.0000 NULL 108.0000 1 2.000 1.0000 ev1 110.0000 0 2.000 1.0000 NULL 112.0000 1 2.000 1.0000 ev1 114.0000 0 2.000 1.0000 NULL 116.0000 2 2.000 1.0000 ev2 118.0000 0 2.000 1.0000 NULL 120.0000 1 2.000 1.0000 ev1 122.0000 0 2.000 1.0000 NULL 124.0000 2 2.000 1.0000 ev2 126.0000 0 2.000 1.0000 NULL 128.0000 2 2.000 1.0000 ev2 130.0000 0 2.000 1.0000 NULL 132.0000 2 2.000 1.0000 ev2 134.0000 0 2.000 1.0000 NULL 136.0000 1 2.000 1.0000 ev1 138.0000 0 2.000 1.0000 NULL 140.0000 2 2.000 1.0000 ev2 142.0000 0 2.000 1.0000 NULL 144.0000 2 2.000 1.0000 ev2 146.0000 0 2.000 1.0000 NULL 148.0000 2 2.000 1.0000 ev2 150.0000 0 2.000 1.0000 NULL 152.0000 2 2.000 1.0000 ev2 154.0000 0 2.000 1.0000 NULL 156.0000 1 2.000 1.0000 ev1 158.0000 0 2.000 1.0000 NULL 160.0000 2 2.000 1.0000 ev2 162.0000 0 2.000 1.0000 NULL 164.0000 2 2.000 1.0000 ev2 166.0000 0 2.000 1.0000 NULL 168.0000 1 2.000 1.0000 ev1 170.0000 0 2.000 1.0000 NULL 172.0000 2 2.000 1.0000 ev2 174.0000 0 2.000 1.0000 NULL 176.0000 1 2.000 1.0000 ev1 178.0000 0 2.000 1.0000 NULL 180.0000 2 2.000 1.0000 ev2 182.0000 0 2.000 1.0000 NULL 184.0000 2 2.000 1.0000 ev2 186.0000 0 2.000 1.0000 NULL 188.0000 1 2.000 1.0000 ev1 190.0000 0 2.000 1.0000 NULL 192.0000 1 2.000 1.0000 ev1 194.0000 0 2.000 1.0000 NULL 196.0000 1 2.000 1.0000 ev1 198.0000 0 2.000 1.0000 NULL 200.0000 1 2.000 1.0000 ev1 202.0000 0 2.000 1.0000 NULL 204.0000 2 2.000 1.0000 ev2 206.0000 0 2.000 1.0000 NULL 208.0000 2 2.000 1.0000 ev2 210.0000 0 2.000 1.0000 NULL 212.0000 2 2.000 1.0000 ev2 214.0000 0 2.000 1.0000 NULL 216.0000 1 2.000 1.0000 ev1 218.0000 0 2.000 1.0000 NULL 220.0000 1 2.000 1.0000 ev1 222.0000 0 2.000 1.0000 NULL 224.0000 1 2.000 1.0000 ev1 226.0000 0 2.000 1.0000 NULL 228.0000 1 2.000 1.0000 ev1 230.0000 0 2.000 1.0000 NULL 232.0000 1 2.000 1.0000 ev1 234.0000 0 2.000 1.0000 NULL 236.0000 1 2.000 1.0000 ev1 238.0000 0 2.000 1.0000 NULL 240.0000 2 2.000 1.0000 ev2 242.0000 0 2.000 1.0000 NULL 244.0000 1 2.000 1.0000 ev1 246.0000 0 2.000 1.0000 NULL 248.0000 1 2.000 1.0000 ev1 250.0000 0 2.000 1.0000 NULL 252.0000 2 2.000 1.0000 ev2 254.0000 0 2.000 1.0000 NULL 256.0000 1 2.000 1.0000 ev1 258.0000 0 2.000 1.0000 NULL 260.0000 2 2.000 1.0000 ev2 262.0000 0 2.000 1.0000 NULL 264.0000 2 2.000 1.0000 ev2 266.0000 0 2.000 1.0000 NULL 268.0000 2 2.000 1.0000 ev2 270.0000 0 2.000 1.0000 NULL 272.0000 1 2.000 1.0000 ev1 274.0000 0 2.000 1.0000 NULL 276.0000 2 2.000 1.0000 ev2 278.0000 0 2.000 1.0000 NULL 280.0000 1 2.000 1.0000 ev1 282.0000 0 2.000 1.0000 NULL 284.0000 1 2.000 1.0000 ev1 286.0000 0 2.000 1.0000 NULL 288.0000 1 2.000 1.0000 ev1 290.0000 0 2.000 1.0000 NULL 292.0000 2 2.000 1.0000 ev2 294.0000 0 2.000 1.0000 NULL 296.0000 2 2.000 1.0000 ev2 298.0000 0 2.000 1.0000 NULL 300.0000 1 2.000 1.0000 ev1 302.0000 0 2.000 1.0000 NULL 304.0000 1 2.000 1.0000 ev1 306.0000 0 2.000 1.0000 NULL 308.0000 2 2.000 1.0000 ev2 310.0000 0 2.000 1.0000 NULL 312.0000 2 2.000 1.0000 ev2 0.0000 2 2.000 1.0000 ev2 0.0000 1 2.000 1.0000 ev1 2.0000 0 322.000 1.0000 NULL ============================================ All time set is 1 TR except last three lines. Where am I wrong? Here is my command: optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 41 --ev ev2 2 40 --nkeep 2 --o ex1 --nsearch 1000 --tnullmin 2 --tnullmax 8 Thanks. All the best. Rujing Zha
2014-06-20
charujing123
发件人：Douglas Greve greve@nmr.mgh.harvard.edu 发送时间：2014-06-20 22:19 主题：Re: [Freesurfer] some questions about optseq 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
On 6/20/14 4:14 PM, charujing123 wrote:
Hi doug, Thanks doug. Here are two questions that I am not sure: 1, Each stimulus condition has three elements, i.e. cue fixation and picture. However it is only picture element that will be analyzed. The time window of picture will not influence the efficiency of sequence? Not much
2, After stimulus presented(last 1.5s), subjects will response to the picture in the specific time window. This time window followed the stimulus, and it varied from 2.5s to ~8.5s. However, some trials was not followed by NULL trial. That is to say, there is no time to response after some trials. You can create a minimum fixed amount of after the trial with --tnullmin doug
Thanks All the best Rujing Zha
2014-06-20
charujing123
发 件人：Douglas Greve greve@nmr.mgh.harvard.edu 发 送时间：2014-06-20 21:18 主 题：Re: [Freesurfer] some questions about optseq 收 件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄 送：
I don't think there is anything wrong with what you have. Is there a problem? You could shorten it to something like 240sec or so.
On 6/20/14 1:43 PM, charujing123 wrote:
Hi doug, Thanks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha
2014-06-20
charujing123
发 件人：Douglas Greve greve@nmr.mgh.harvard.edu 发 送时间：2014-06-20 16:51 主 题：Re: [Freesurfer] some questions about optseq 收 件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄 送：
I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order
On 6/20/14 4:27 AM, charujing123 wrote:
Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20
charujing123
_______________________________________________ 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
weird? I'll need something more specific than that
On 6/20/14 4:57 PM, charujing123 wrote:
Hi doug Thanks very much. I see. When I add --tnullmin 2 --tnullmax 8, result looks weird. ======================================= [psylab16@centos1 ~]$ cat ex1-001.par 0.0000 2 2.000 1.0000 ev2 2.0000 0 2.000 1.0000 NULL 4.0000 1 2.000 1.0000 ev1 6.0000 0 2.000 1.0000 NULL 8.0000 1 2.000 1.0000 ev1 10.0000 0 2.000 1.0000 NULL 12.0000 1 2.000 1.0000 ev1 14.0000 0 2.000 1.0000 NULL 16.0000 1 2.000 1.0000 ev1 18.0000 0 2.000 1.0000 NULL 20.0000 2 2.000 1.0000 ev2 22.0000 0 2.000 1.0000 NULL 24.0000 1 2.000 1.0000 ev1 26.0000 0 2.000 1.0000 NULL 28.0000 1 2.000 1.0000 ev1 30.0000 0 2.000 1.0000 NULL 32.0000 2 2.000 1.0000 ev2 34.0000 0 2.000 1.0000 NULL 36.0000 2 2.000 1.0000 ev2 38.0000 0 2.000 1.0000 NULL 40.0000 2 2.000 1.0000 ev2 42.0000 0 2.000 1.0000 NULL 44.0000 2 2.000 1.0000 ev2 46.0000 0 2.000 1.0000 NULL 48.0000 1 2.000 1.0000 ev1 50.0000 0 2.000 1.0000 NULL 52.0000 2 2.000 1.0000 ev2 54.0000 0 2.000 1.0000 NULL 56.0000 1 2.000 1.0000 ev1 58.0000 0 2.000 1.0000 NULL 60.0000 2 2.000 1.0000 ev2 62.0000 0 2.000 1.0000 NULL 64.0000 2 2.000 1.0000 ev2 66.0000 0 2.000 1.0000 NULL 68.0000 1 2.000 1.0000 ev1 70.0000 0 2.000 1.0000 NULL 72.0000 1 2.000 1.0000 ev1 74.0000 0 2.000 1.0000 NULL 76.0000 1 2.000 1.0000 ev1 78.0000 0 2.000 1.0000 NULL 80.0000 2 2.000 1.0000 ev2 82.0000 0 2.000 1.0000 NULL 84.0000 2 2.000 1.0000 ev2 86.0000 0 2.000 1.0000 NULL 88.0000 2 2.000 1.0000 ev2 90.0000 0 2.000 1.0000 NULL 92.0000 1 2.000 1.0000 ev1 94.0000 0 2.000 1.0000 NULL 96.0000 1 2.000 1.0000 ev1 98.0000 0 2.000 1.0000 NULL 100.0000 1 2.000 1.0000 ev1 102.0000 0 2.000 1.0000 NULL 104.0000 2 2.000 1.0000 ev2 106.0000 0 2.000 1.0000 NULL 108.0000 1 2.000 1.0000 ev1 110.0000 0 2.000 1.0000 NULL 112.0000 1 2.000 1.0000 ev1 114.0000 0 2.000 1.0000 NULL 116.0000 2 2.000 1.0000 ev2 118.0000 0 2.000 1.0000 NULL 120.0000 1 2.000 1.0000 ev1 122.0000 0 2.000 1.0000 NULL 124.0000 2 2.000 1.0000 ev2 126.0000 0 2.000 1.0000 NULL 128.0000 2 2.000 1.0000 ev2 130.0000 0 2.000 1.0000 NULL 132.0000 2 2.000 1.0000 ev2 134.0000 0 2.000 1.0000 NULL 136.0000 1 2.000 1.0000 ev1 138.0000 0 2.000 1.0000 NULL 140.0000 2 2.000 1.0000 ev2 142.0000 0 2.000 1.0000 NULL 144.0000 2 2.000 1.0000 ev2 146.0000 0 2.000 1.0000 NULL 148.0000 2 2.000 1.0000 ev2 150.0000 0 2.000 1.0000 NULL 152.0000 2 2.000 1.0000 ev2 154.0000 0 2.000 1.0000 NULL 156.0000 1 2.000 1.0000 ev1 158.0000 0 2.000 1.0000 NULL 160.0000 2 2.000 1.0000 ev2 162.0000 0 2.000 1.0000 NULL 164.0000 2 2.000 1.0000 ev2 166.0000 0 2.000 1.0000 NULL 168.0000 1 2.000 1.0000 ev1 170.0000 0 2.000 1.0000 NULL 172.0000 2 2.000 1.0000 ev2 174.0000 0 2.000 1.0000 NULL 176.0000 1 2.000 1.0000 ev1 178.0000 0 2.000 1.0000 NULL 180.0000 2 2.000 1.0000 ev2 182.0000 0 2.000 1.0000 NULL 184.0000 2 2.000 1.0000 ev2 186.0000 0 2.000 1.0000 NULL 188.0000 1 2.000 1.0000 ev1 190.0000 0 2.000 1.0000 NULL 192.0000 1 2.000 1.0000 ev1 194.0000 0 2.000 1.0000 NULL 196.0000 1 2.000 1.0000 ev1 198.0000 0 2.000 1.0000 NULL 200.0000 1 2.000 1.0000 ev1 202.0000 0 2.000 1.0000 NULL 204.0000 2 2.000 1.0000 ev2 206.0000 0 2.000 1.0000 NULL 208.0000 2 2.000 1.0000 ev2 210.0000 0 2.000 1.0000 NULL 212.0000 2 2.000 1.0000 ev2 214.0000 0 2.000 1.0000 NULL 216.0000 1 2.000 1.0000 ev1 218.0000 0 2.000 1.0000 NULL 220.0000 1 2.000 1.0000 ev1 222.0000 0 2.000 1.0000 NULL 224.0000 1 2.000 1.0000 ev1 226.0000 0 2.000 1.0000 NULL 228.0000 1 2.000 1.0000 ev1 230.0000 0 2.000 1.0000 NULL 232.0000 1 2.000 1.0000 ev1 234.0000 0 2.000 1.0000 NULL 236.0000 1 2.000 1.0000 ev1 238.0000 0 2.000 1.0000 NULL 240.0000 2 2.000 1.0000 ev2 242.0000 0 2.000 1.0000 NULL 244.0000 1 2.000 1.0000 ev1 246.0000 0 2.000 1.0000 NULL 248.0000 1 2.000 1.0000 ev1 250.0000 0 2.000 1.0000 NULL 252.0000 2 2.000 1.0000 ev2 254.0000 0 2.000 1.0000 NULL 256.0000 1 2.000 1.0000 ev1 258.0000 0 2.000 1.0000 NULL 260.0000 2 2.000 1.0000 ev2 262.0000 0 2.000 1.0000 NULL 264.0000 2 2.000 1.0000 ev2 266.0000 0 2.000 1.0000 NULL 268.0000 2 2.000 1.0000 ev2 270.0000 0 2.000 1.0000 NULL 272.0000 1 2.000 1.0000 ev1 274.0000 0 2.000 1.0000 NULL 276.0000 2 2.000 1.0000 ev2 278.0000 0 2.000 1.0000 NULL 280.0000 1 2.000 1.0000 ev1 282.0000 0 2.000 1.0000 NULL 284.0000 1 2.000 1.0000 ev1 286.0000 0 2.000 1.0000 NULL 288.0000 1 2.000 1.0000 ev1 290.0000 0 2.000 1.0000 NULL 292.0000 2 2.000 1.0000 ev2 294.0000 0 2.000 1.0000 NULL 296.0000 2 2.000 1.0000 ev2 298.0000 0 2.000 1.0000 NULL 300.0000 1 2.000 1.0000 ev1 302.0000 0 2.000 1.0000 NULL 304.0000 1 2.000 1.0000 ev1 306.0000 0 2.000 1.0000 NULL 308.0000 2 2.000 1.0000 ev2 310.0000 0 2.000 1.0000 NULL 312.0000 2 2.000 1.0000 ev2 0.0000 2 2.000 1.0000 ev2 0.0000 1 2.000 1.0000 ev1 2.0000 0 322.000 1.0000 NULL ============================================ All time set is 1 TR except last three lines. Where am I wrong? Here is my command: optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 41 --ev ev2 2 40 --nkeep 2 --o ex1 --nsearch 1000 --tnullmin 2 --tnullmax 8 Thanks. All the best. Rujing Zha 2014-06-20
charujing123
*? ??:*Douglas Greve greve@nmr.mgh.harvard.edu *? ???:*2014-06-20 22:19 *? ?:*Re: [Freesurfer] some questions about optseq *? ??:*"freesurfer"freesurfer@nmr.mgh.harvard.edu *? ?:*
On 6/20/14 4:14 PM, charujing123 wrote:
Hi doug, Thanks doug. Here are two questions that I am not sure: 1, Each stimulus condition has three elements, i.e. cue fixation and picture. However it is only picture element that will be analyzed. The time window of picture will not influence the efficiency of sequence?
Not much
2, After stimulus presented(last 1.5s), subjects will response to the picture in the specific time window. This time window followed the stimulus, and it varied from 2.5s to ~8.5s. However, some trials was not followed by NULL trial. That is to say, there is no time to response after some trials.
You can create a minimum fixed amount of after the trial with --tnullmin doug
Thanks All the best Rujing Zha 2014-06-20
charujing123
*? ??:*Douglas Greve greve@nmr.mgh.harvard.edu *? ???:*2014-06-20 21:18 *? ?:*Re: [Freesurfer] some questions about optseq *? ??:*"freesurfer"freesurfer@nmr.mgh.harvard.edu *? ?:*
I don't think there is anything wrong with what you have. Is there a problem? You could shorten it to something like 240sec or so.
On 6/20/14 1:43 PM, charujing123 wrote:
Hi doug, Th?anks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha 2014-06-20
charujing123
*? ??:*Douglas Greve greve@nmr.mgh.harvard.edu *? ???:*2014-06-20 16:51 *? ?:*Re: [Freesurfer] some questions about optseq *? ??:*"freesurfer"freesurfer@nmr.mgh.harvard.edu *? ?:*
I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order
On 6/20/14 4:27 AM, charujing123 wrote:
Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20
charujing123
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi doug, sorry for not enough information sending to you. optseq2 --ntp 223 --tr 2 --psdwin 0 20 --ev ev1 2 41 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 --tnullmin 2 --tnullmax 8 After running the command above, I get the ex2-001.par and ex2-002.par. In these files, I found that part of NULL window had 10s intervals. However I set the --tnullmax 8, the max time window of NULL should be 8s, not 10s, shouldnot it? Also I check the help of optseq2, and it echo " Note: it may not be possible for a given parameter set to keep the NULL stimulus below a certain amount. In this case, the following error message will be printed out 'ERROR: could not enforce tNullMax'. By default, tNullMax is infinite." But I didnot find any ERROR information in the command window. Is that normal? Thanks All the best Rujing Zha 2014-06-21
charujing123
发件人：Douglas Greve greve@nmr.mgh.harvard.edu 发送时间：2014-06-20 23:21 主题：Re: [Freesurfer] some questions about optseq 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
weird? I'll need something more specific than that
On 6/20/14 4:57 PM, charujing123 wrote:
Hi doug Thanks very much. I see. When I add --tnullmin 2 --tnullmax 8, result looks weird. ======================================= [psylab16@centos1 ~]$ cat ex1-001.par 0.0000 2 2.000 1.0000 ev2 2.0000 0 2.000 1.0000 NULL 4.0000 1 2.000 1.0000 ev1 6.0000 0 2.000 1.0000 NULL 8.0000 1 2.000 1.0000 ev1 10.0000 0 2.000 1.0000 NULL 12.0000 1 2.000 1.0000 ev1 14.0000 0 2.000 1.0000 NULL 16.0000 1 2.000 1.0000 ev1 18.0000 0 2.000 1.0000 NULL 20.0000 2 2.000 1.0000 ev2 22.0000 0 2.000 1.0000 NULL 24.0000 1 2.000 1.0000 ev1 26.0000 0 2.000 1.0000 NULL 28.0000 1 2.000 1.0000 ev1 30.0000 0 2.000 1.0000 NULL 32.0000 2 2.000 1.0000 ev2 34.0000 0 2.000 1.0000 NULL 36.0000 2 2.000 1.0000 ev2 38.0000 0 2.000 1.0000 NULL 40.0000 2 2.000 1.0000 ev2 42.0000 0 2.000 1.0000 NULL 44.0000 2 2.000 1.0000 ev2 46.0000 0 2.000 1.0000 NULL 48.0000 1 2.000 1.0000 ev1 50.0000 0 2.000 1.0000 NULL 52.0000 2 2.000 1.0000 ev2 54.0000 0 2.000 1.0000 NULL 56.0000 1 2.000 1.0000 ev1 58.0000 0 2.000 1.0000 NULL 60.0000 2 2.000 1.0000 ev2 62.0000 0 2.000 1.0000 NULL 64.0000 2 2.000 1.0000 ev2 66.0000 0 2.000 1.0000 NULL 68.0000 1 2.000 1.0000 ev1 70.0000 0 2.000 1.0000 NULL 72.0000 1 2.000 1.0000 ev1 74.0000 0 2.000 1.0000 NULL 76.0000 1 2.000 1.0000 ev1 78.0000 0 2.000 1.0000 NULL 80.0000 2 2.000 1.0000 ev2 82.0000 0 2.000 1.0000 NULL 84.0000 2 2.000 1.0000 ev2 86.0000 0 2.000 1.0000 NULL 88.0000 2 2.000 1.0000 ev2 90.0000 0 2.000 1.0000 NULL 92.0000 1 2.000 1.0000 ev1 94.0000 0 2.000 1.0000 NULL 96.0000 1 2.000 1.0000 ev1 98.0000 0 2.000 1.0000 NULL 100.0000 1 2.000 1.0000 ev1 102.0000 0 2.000 1.0000 NULL 104.0000 2 2.000 1.0000 ev2 106.0000 0 2.000 1.0000 NULL 108.0000 1 2.000 1.0000 ev1 110.0000 0 2.000 1.0000 NULL 112.0000 1 2.000 1.0000 ev1 114.0000 0 2.000 1.0000 NULL 116.0000 2 2.000 1.0000 ev2 118.0000 0 2.000 1.0000 NULL 120.0000 1 2.000 1.0000 ev1 122.0000 0 2.000 1.0000 NULL 124.0000 2 2.000 1.0000 ev2 126.0000 0 2.000 1.0000 NULL 128.0000 2 2.000 1.0000 ev2 130.0000 0 2.000 1.0000 NULL 132.0000 2 2.000 1.0000 ev2 134.0000 0 2.000 1.0000 NULL 136.0000 1 2.000 1.0000 ev1 138.0000 0 2.000 1.0000 NULL 140.0000 2 2.000 1.0000 ev2 142.0000 0 2.000 1.0000 NULL 144.0000 2 2.000 1.0000 ev2 146.0000 0 2.000 1.0000 NULL 148.0000 2 2.000 1.0000 ev2 150.0000 0 2.000 1.0000 NULL 152.0000 2 2.000 1.0000 ev2 154.0000 0 2.000 1.0000 NULL 156.0000 1 2.000 1.0000 ev1 158.0000 0 2.000 1.0000 NULL 160.0000 2 2.000 1.0000 ev2 162.0000 0 2.000 1.0000 NULL 164.0000 2 2.000 1.0000 ev2 166.0000 0 2.000 1.0000 NULL 168.0000 1 2.000 1.0000 ev1 170.0000 0 2.000 1.0000 NULL 172.0000 2 2.000 1.0000 ev2 174.0000 0 2.000 1.0000 NULL 176.0000 1 2.000 1.0000 ev1 178.0000 0 2.000 1.0000 NULL 180.0000 2 2.000 1.0000 ev2 182.0000 0 2.000 1.0000 NULL 184.0000 2 2.000 1.0000 ev2 186.0000 0 2.000 1.0000 NULL 188.0000 1 2.000 1.0000 ev1 190.0000 0 2.000 1.0000 NULL 192.0000 1 2.000 1.0000 ev1 194.0000 0 2.000 1.0000 NULL 196.0000 1 2.000 1.0000 ev1 198.0000 0 2.000 1.0000 NULL 200.0000 1 2.000 1.0000 ev1 202.0000 0 2.000 1.0000 NULL 204.0000 2 2.000 1.0000 ev2 206.0000 0 2.000 1.0000 NULL 208.0000 2 2.000 1.0000 ev2 210.0000 0 2.000 1.0000 NULL 212.0000 2 2.000 1.0000 ev2 214.0000 0 2.000 1.0000 NULL 216.0000 1 2.000 1.0000 ev1 218.0000 0 2.000 1.0000 NULL 220.0000 1 2.000 1.0000 ev1 222.0000 0 2.000 1.0000 NULL 224.0000 1 2.000 1.0000 ev1 226.0000 0 2.000 1.0000 NULL 228.0000 1 2.000 1.0000 ev1 230.0000 0 2.000 1.0000 NULL 232.0000 1 2.000 1.0000 ev1 234.0000 0 2.000 1.0000 NULL 236.0000 1 2.000 1.0000 ev1 238.0000 0 2.000 1.0000 NULL 240.0000 2 2.000 1.0000 ev2 242.0000 0 2.000 1.0000 NULL 244.0000 1 2.000 1.0000 ev1 246.0000 0 2.000 1.0000 NULL 248.0000 1 2.000 1.0000 ev1 250.0000 0 2.000 1.0000 NULL 252.0000 2 2.000 1.0000 ev2 254.0000 0 2.000 1.0000 NULL 256.0000 1 2.000 1.0000 ev1 258.0000 0 2.000 1.0000 NULL 260.0000 2 2.000 1.0000 ev2 262.0000 0 2.000 1.0000 NULL 264.0000 2 2.000 1.0000 ev2 266.0000 0 2.000 1.0000 NULL 268.0000 2 2.000 1.0000 ev2 270.0000 0 2.000 1.0000 NULL 272.0000 1 2.000 1.0000 ev1 274.0000 0 2.000 1.0000 NULL 276.0000 2 2.000 1.0000 ev2 278.0000 0 2.000 1.0000 NULL 280.0000 1 2.000 1.0000 ev1 282.0000 0 2.000 1.0000 NULL 284.0000 1 2.000 1.0000 ev1 286.0000 0 2.000 1.0000 NULL 288.0000 1 2.000 1.0000 ev1 290.0000 0 2.000 1.0000 NULL 292.0000 2 2.000 1.0000 ev2 294.0000 0 2.000 1.0000 NULL 296.0000 2 2.000 1.0000 ev2 298.0000 0 2.000 1.0000 NULL 300.0000 1 2.000 1.0000 ev1 302.0000 0 2.000 1.0000 NULL 304.0000 1 2.000 1.0000 ev1 306.0000 0 2.000 1.0000 NULL 308.0000 2 2.000 1.0000 ev2 310.0000 0 2.000 1.0000 NULL 312.0000 2 2.000 1.0000 ev2 0.0000 2 2.000 1.0000 ev2 0.0000 1 2.000 1.0000 ev1 2.0000 0 322.000 1.0000 NULL ============================================ All time set is 1 TR except last three lines. Where am I wrong? Here is my command: optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 41 --ev ev2 2 40 --nkeep 2 --o ex1 --nsearch 1000 --tnullmin 2 --tnullmax 8 Thanks. All the best. Rujing Zha
2014-06-20
charujing123
发 件人：Douglas Greve greve@nmr.mgh.harvard.edu 发 送时间：2014-06-20 22:19 主 题：Re: [Freesurfer] some questions about optseq 收 件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄 送：
On 6/20/14 4:14 PM, charujing123 wrote:
Hi doug, Thanks doug. Here are two questions that I am not sure: 1, Each stimulus condition has three elements, i.e. cue fixation and picture. However it is only picture element that will be analyzed. The time window of picture will not influence the efficiency of sequence? Not much
2, After stimulus presented(last 1.5s), subjects will response to the picture in the specific time window. This time window followed the stimulus, and it varied from 2.5s to ~8.5s. However, some trials was not followed by NULL trial. That is to say, there is no time to response after some trials. You can create a minimum fixed amount of after the trial with --tnullmin doug
Thanks All the best Rujing Zha
2014-06-20
charujing123
发 件人：Douglas Greve greve@nmr.mgh.harvard.edu 发 送时间：2014-06-20 21:18 主 题：Re: [Freesurfer] some questions about optseq 收 件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄 送：
I don't think there is anything wrong with what you have. Is there a problem? You could shorten it to something like 240sec or so.
On 6/20/14 1:43 PM, charujing123 wrote:
Hi doug, Thanks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha
2014-06-20
charujing123
发 件人：Douglas Greve greve@nmr.mgh.harvard.edu 发 送时间：2014-06-20 16:51 主 题：Re: [Freesurfer] some questions about optseq 收 件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄 送：
I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order
On 6/20/14 4:27 AM, charujing123 wrote:
Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20
charujing123
_______________________________________________ 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I think this is an error I fixed a few months ago. Try this version (for linux) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/optseq2
On 06/20/2014 09:05 PM, charujing123 wrote:
Hi doug, sorry for not enough information sending to you. optseq2 --ntp 223 --tr 2 --psdwin 0 20 --ev ev1 2 41 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 --tnullmin 2 --tnullmax 8 After running the command above, I get the ex2-001.par and ex2-002.par. In these files, I found that part of NULL window had 10s intervals. However I set the --tnullmax 8, the max time window of NULL should be 8s, not 10s, shouldnot it? Also I check the help of optseq2, and it echo " Note: it may not be possible for a given parameter set to keep the NULL stimulus below a certain amount. In this case, the following error message will be printed out 'ERROR: could not enforce tNullMax'. By default, tNullMax is infinite." But I didnot find any ERROR information in the command window. Is that normal? Thanks All the best Rujing Zha 2014-06-21
charujing123
*发 件人：*Douglas Greve greve@nmr.mgh.harvard.edu *发 送时间：*2014-06-20 23:21 *主 题：*Re: [Freesurfer] some questions about optseq *收 件人：*"freesurfer"freesurfer@nmr.mgh.harvard.edu *抄 送：*
weird? I'll need something more specific than that
On 6/20/14 4:57 PM, charujing123 wrote:
Hi doug Thanks very much. I see. When I add --tnullmin 2 --tnullmax 8, result looks weird. ======================================= [psylab16@centos1 ~]$ cat ex1-001.par 0.0000 2 2.000 1.0000 ev2 2.0000 0 2.000 1.0000 NULL 4.0000 1 2.000 1.0000 ev1 6.0000 0 2.000 1.0000 NULL 8.0000 1 2.000 1.0000 ev1 10.0000 0 2.000 1.0000 NULL 12.0000 1 2.000 1.0000 ev1 14.0000 0 2.000 1.0000 NULL 16.0000 1 2.000 1.0000 ev1 18.0000 0 2.000 1.0000 NULL 20.0000 2 2.000 1.0000 ev2 22.0000 0 2.000 1.0000 NULL 24.0000 1 2.000 1.0000 ev1 26.0000 0 2.000 1.0000 NULL 28.0000 1 2.000 1.0000 ev1 30.0000 0 2.000 1.0000 NULL 32.0000 2 2.000 1.0000 ev2 34.0000 0 2.000 1.0000 NULL 36.0000 2 2.000 1.0000 ev2 38.0000 0 2.000 1.0000 NULL 40.0000 2 2.000 1.0000 ev2 42.0000 0 2.000 1.0000 NULL 44.0000 2 2.000 1.0000 ev2 46.0000 0 2.000 1.0000 NULL 48.0000 1 2.000 1.0000 ev1 50.0000 0 2.000 1.0000 NULL 52.0000 2 2.000 1.0000 ev2 54.0000 0 2.000 1.0000 NULL 56.0000 1 2.000 1.0000 ev1 58.0000 0 2.000 1.0000 NULL 60.0000 2 2.000 1.0000 ev2 62.0000 0 2.000 1.0000 NULL 64.0000 2 2.000 1.0000 ev2 66.0000 0 2.000 1.0000 NULL 68.0000 1 2.000 1.0000 ev1 70.0000 0 2.000 1.0000 NULL 72.0000 1 2.000 1.0000 ev1 74.0000 0 2.000 1.0000 NULL 76.0000 1 2.000 1.0000 ev1 78.0000 0 2.000 1.0000 NULL 80.0000 2 2.000 1.0000 ev2 82.0000 0 2.000 1.0000 NULL 84.0000 2 2.000 1.0000 ev2 86.0000 0 2.000 1.0000 NULL 88.0000 2 2.000 1.0000 ev2 90.0000 0 2.000 1.0000 NULL 92.0000 1 2.000 1.0000 ev1 94.0000 0 2.000 1.0000 NULL 96.0000 1 2.000 1.0000 ev1 98.0000 0 2.000 1.0000 NULL 100.0000 1 2.000 1.0000 ev1 102.0000 0 2.000 1.0000 NULL 104.0000 2 2.000 1.0000 ev2 106.0000 0 2.000 1.0000 NULL 108.0000 1 2.000 1.0000 ev1 110.0000 0 2.000 1.0000 NULL 112.0000 1 2.000 1.0000 ev1 114.0000 0 2.000 1.0000 NULL 116.0000 2 2.000 1.0000 ev2 118.0000 0 2.000 1.0000 NULL 120.0000 1 2.000 1.0000 ev1 122.0000 0 2.000 1.0000 NULL 124.0000 2 2.000 1.0000 ev2 126.0000 0 2.000 1.0000 NULL 128.0000 2 2.000 1.0000 ev2 130.0000 0 2.000 1.0000 NULL 132.0000 2 2.000 1.0000 ev2 134.0000 0 2.000 1.0000 NULL 136.0000 1 2.000 1.0000 ev1 138.0000 0 2.000 1.0000 NULL 140.0000 2 2.000 1.0000 ev2 142.0000 0 2.000 1.0000 NULL 144.0000 2 2.000 1.0000 ev2 146.0000 0 2.000 1.0000 NULL 148.0000 2 2.000 1.0000 ev2 150.0000 0 2.000 1.0000 NULL 152.0000 2 2.000 1.0000 ev2 154.0000 0 2.000 1.0000 NULL 156.0000 1 2.000 1.0000 ev1 158.0000 0 2.000 1.0000 NULL 160.0000 2 2.000 1.0000 ev2 162.0000 0 2.000 1.0000 NULL 164.0000 2 2.000 1.0000 ev2 166.0000 0 2.000 1.0000 NULL 168.0000 1 2.000 1.0000 ev1 170.0000 0 2.000 1.0000 NULL 172.0000 2 2.000 1.0000 ev2 174.0000 0 2.000 1.0000 NULL 176.0000 1 2.000 1.0000 ev1 178.0000 0 2.000 1.0000 NULL 180.0000 2 2.000 1.0000 ev2 182.0000 0 2.000 1.0000 NULL 184.0000 2 2.000 1.0000 ev2 186.0000 0 2.000 1.0000 NULL 188.0000 1 2.000 1.0000 ev1 190.0000 0 2.000 1.0000 NULL 192.0000 1 2.000 1.0000 ev1 194.0000 0 2.000 1.0000 NULL 196.0000 1 2.000 1.0000 ev1 198.0000 0 2.000 1.0000 NULL 200.0000 1 2.000 1.0000 ev1 202.0000 0 2.000 1.0000 NULL 204.0000 2 2.000 1.0000 ev2 206.0000 0 2.000 1.0000 NULL 208.0000 2 2.000 1.0000 ev2 210.0000 0 2.000 1.0000 NULL 212.0000 2 2.000 1.0000 ev2 214.0000 0 2.000 1.0000 NULL 216.0000 1 2.000 1.0000 ev1 218.0000 0 2.000 1.0000 NULL 220.0000 1 2.000 1.0000 ev1 222.0000 0 2.000 1.0000 NULL 224.0000 1 2.000 1.0000 ev1 226.0000 0 2.000 1.0000 NULL 228.0000 1 2.000 1.0000 ev1 230.0000 0 2.000 1.0000 NULL 232.0000 1 2.000 1.0000 ev1 234.0000 0 2.000 1.0000 NULL 236.0000 1 2.000 1.0000 ev1 238.0000 0 2.000 1.0000 NULL 240.0000 2 2.000 1.0000 ev2 242.0000 0 2.000 1.0000 NULL 244.0000 1 2.000 1.0000 ev1 246.0000 0 2.000 1.0000 NULL 248.0000 1 2.000 1.0000 ev1 250.0000 0 2.000 1.0000 NULL 252.0000 2 2.000 1.0000 ev2 254.0000 0 2.000 1.0000 NULL 256.0000 1 2.000 1.0000 ev1 258.0000 0 2.000 1.0000 NULL 260.0000 2 2.000 1.0000 ev2 262.0000 0 2.000 1.0000 NULL 264.0000 2 2.000 1.0000 ev2 266.0000 0 2.000 1.0000 NULL 268.0000 2 2.000 1.0000 ev2 270.0000 0 2.000 1.0000 NULL 272.0000 1 2.000 1.0000 ev1 274.0000 0 2.000 1.0000 NULL 276.0000 2 2.000 1.0000 ev2 278.0000 0 2.000 1.0000 NULL 280.0000 1 2.000 1.0000 ev1 282.0000 0 2.000 1.0000 NULL 284.0000 1 2.000 1.0000 ev1 286.0000 0 2.000 1.0000 NULL 288.0000 1 2.000 1.0000 ev1 290.0000 0 2.000 1.0000 NULL 292.0000 2 2.000 1.0000 ev2 294.0000 0 2.000 1.0000 NULL 296.0000 2 2.000 1.0000 ev2 298.0000 0 2.000 1.0000 NULL 300.0000 1 2.000 1.0000 ev1 302.0000 0 2.000 1.0000 NULL 304.0000 1 2.000 1.0000 ev1 306.0000 0 2.000 1.0000 NULL 308.0000 2 2.000 1.0000 ev2 310.0000 0 2.000 1.0000 NULL 312.0000 2 2.000 1.0000 ev2 0.0000 2 2.000 1.0000 ev2 0.0000 1 2.000 1.0000 ev1 2.0000 0 322.000 1.0000 NULL ============================================ All time set is 1 TR except last three lines. Where am I wrong? Here is my command: optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 41 --ev ev2 2 40 --nkeep 2 --o ex1 --nsearch 1000 --tnullmin 2 --tnullmax 8 Thanks. All the best. Rujing Zha 2014-06-20
charujing123
*发 件人：*Douglas Greve greve@nmr.mgh.harvard.edu *发 送时间：*2014-06-20 22:19 *主 题：*Re: [Freesurfer] some questions about optseq *收 件人：*"freesurfer"freesurfer@nmr.mgh.harvard.edu *抄 送：*
On 6/20/14 4:14 PM, charujing123 wrote:
Hi doug, Thanks doug. Here are two questions that I am not sure: 1, Each stimulus condition has three elements, i.e. cue fixation and picture. However it is only picture element that will be analyzed. The time window of picture will not influence the efficiency of sequence?
Not much
2, After stimulus presented(last 1.5s), subjects will response to the picture in the specific time window. This time window followed the stimulus, and it varied from 2.5s to ~8.5s. However, some trials was not followed by NULL trial. That is to say, there is no time to response after some trials.
You can create a minimum fixed amount of after the trial with --tnullmin doug
Thanks All the best Rujing Zha 2014-06-20
charujing123
*发 件人：*Douglas Greve greve@nmr.mgh.harvard.edu *发 送时间：*2014-06-20 21:18 *主 题：*Re: [Freesurfer] some questions about optseq *收 件人：*"freesurfer"freesurfer@nmr.mgh.harvard.edu *抄 送：*
I don't think there is anything wrong with what you have. Is there a problem? You could shorten it to something like 240sec or so.
On 6/20/14 1:43 PM, charujing123 wrote:
Hi doug, Thanks doug. In our experiment, there are 324s, and TR=2s, two kinds of stimulus. Each one consisted of 3 components(cue 500ms + fixation 500ms + picture 500ms), and will be presented with a interval of 1.5s. After stimulus onset, followed by reaction time. One stimulus will repeat 41 times, the other 40 times. Based on optseq2 --ntp 162 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000, how should I modify to get a efficient sequence, as I have no idea about NULL design. Thanks again All the best Rujing Zha 2014-06-20
charujing123
*发 件人：*Douglas Greve greve@nmr.mgh.harvard.edu *发 送时间：*2014-06-20 16:51 *主 题：*Re: [Freesurfer] some questions about optseq *收 件人：*"freesurfer"freesurfer@nmr.mgh.harvard.edu *抄 送：*
I don't understand what you are trying to do. Can you elaborate? There is no way to make optseq produce a sequence where two events always occur in a certain order
On 6/20/14 4:27 AM, charujing123 wrote:
Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20
charujing123
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Hi All, In fs5.3, I tried to generate a volume mask from the pial surface using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg $subjsess/bold/001/register.dof6.dat --template $subjsess/bold/001/template.nii --surf pial --o $subjsess/bold/001/lh.pialmask.vol.nii. The command run successfully. I doubled check the registration between the EPI and high resolution T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898. however, when I overlaid the mask on the T1.mgz, it is clear that some voxels outside brain are in the mask, and some voxels in the gray matter are not in the mask (see attached figure). Did I use the function incorrectly? Thanks very much for your help. Xiaomin
it is hard to tell from that view. Can you click on a point that appears to be outside the brain so we can see what it looks like around that point in all three views?
On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
Hi All,
In fs5.3, I tried to generate a volume mask from the pial surface using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg $subjsess/bold/001/register.dof6.dat --template $subjsess/bold/001/template.nii --surf pial --o $subjsess/bold/001/lh.pialmask.vol.nii. The command run successfully. I doubled check the registration between the EPI and high resolution T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898. however, when I overlaid the mask on the T1.mgz, it is clear that some voxels outside brain are in the mask, and some voxels in the gray matter are not in the mask (see attached figure). Did I use the function incorrectly?
Thanks very much for your help.
Xiaomin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
here it is. thanks,
To: freesurfer@nmr.mgh.harvard.edu From: greve@nmr.mgh.harvard.edu Date: Fri, 15 Jan 2016 12:00:02 -0500 Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
it is hard to tell from that view. Can you click on a point that appears to be outside the brain so we can see what it looks like around that point in all three views?
On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
Hi All,
In fs5.3, I tried to generate a volume mask from the pial surface using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg $subjsess/bold/001/register.dof6.dat --template $subjsess/bold/001/template.nii --surf pial --o $subjsess/bold/001/lh.pialmask.vol.nii. The command run successfully. I doubled check the registration between the EPI and high resolution T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898. however, when I overlaid the mask on the T1.mgz, it is clear that some voxels outside brain are in the mask, and some voxels in the gray matter are not in the mask (see attached figure). Did I use the function incorrectly?
Thanks very much for your help.
Xiaomin
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 greve@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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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.
That point is fairly close to the pial surface. What is your voxel size? It will include any voxel even if only a corner of it has some surface in it.
On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
here it is. thanks,
To: freesurfer@nmr.mgh.harvard.edu From: greve@nmr.mgh.harvard.edu Date: Fri, 15 Jan 2016 12:00:02 -0500 Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
it is hard to tell from that view. Can you click on a point that
appears
to be outside the brain so we can see what it looks like around that point in all three views?
On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
Hi All,
In fs5.3, I tried to generate a volume mask from the pial surface using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg $subjsess/bold/001/register.dof6.dat --template $subjsess/bold/001/template.nii --surf pial --o $subjsess/bold/001/lh.pialmask.vol.nii. The command run successfully. I doubled check the registration between the EPI and high resolution T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898. however, when I overlaid the mask on the T1.mgz, it is clear that some voxels outside brain are in the mask, and some voxels in the
gray
matter are not in the mask (see attached figure). Did I use the function incorrectly?
Thanks very much for your help.
Xiaomin
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 greve@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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The information in this e-mail is intended only for the person to
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HelpLine at
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The voxel size is 1.5mm. Some of voxels in the gray matter are not included in the mask as well. Why? Xiaomin
On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
That point is fairly close to the pial surface. What is your voxel size? It will include any voxel even if only a corner of it has some surface in it.
On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
here it is. thanks,
To: freesurfer@nmr.mgh.harvard.edu From: greve@nmr.mgh.harvard.edu Date: Fri, 15 Jan 2016 12:00:02 -0500 Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
it is hard to tell from that view. Can you click on a point that
appears
to be outside the brain so we can see what it looks like around that point in all three views?
On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
Hi All,
In fs5.3, I tried to generate a volume mask from the pial surface using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg $subjsess/bold/001/register.dof6.dat --template $subjsess/bold/001/template.nii --surf pial --o $subjsess/bold/001/lh.pialmask.vol.nii. The command run successfully. I doubled check the registration between the EPI and high resolution T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898. however, when I overlaid the mask on the T1.mgz, it is clear that some voxels outside brain are in the mask, and some voxels in the
gray
matter are not in the mask (see attached figure). Did I use the function incorrectly?
Thanks very much for your help.
Xiaomin
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 greve@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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HelpLine at
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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 greve@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
I think you could easily hit all those voxels with a 1.5mm voxel size. Not sure what you are asking about in terms of gray matter.
On 01/15/2016 12:27 PM, Xiaomin Yue wrote:
The voxel size is 1.5mm. Some of voxels in the gray matter are not included in the mask as well. Why?
Xiaomin
On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That point is fairly close to the pial surface. What is your voxel size? It will include any voxel even if only a corner of it has some surface in it.
On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
here it is. thanks,
To: freesurfer@nmr.mgh.harvard.edu From: greve@nmr.mgh.harvard.edu Date: Fri, 15 Jan 2016 12:00:02 -0500 Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
it is hard to tell from that view. Can you click on a point that
appears
to be outside the brain so we can see what it looks like around that point in all three views?
On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
Hi All,
In fs5.3, I tried to generate a volume mask from the pial surface using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg $subjsess/bold/001/register.dof6.dat --template $subjsess/bold/001/template.nii --surf pial --o $subjsess/bold/001/lh.pialmask.vol.nii. The command run
successfully.
I doubled check the registration between the EPI and high resolution T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898. however, when I overlaid the mask on the T1.mgz, it is clear that some voxels outside brain are in the mask, and some voxels in the
gray
matter are not in the mask (see attached figure). Did I use the function incorrectly?
Thanks very much for your help.
Xiaomin
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 greve@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
http://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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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 http://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
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Maybe, I misunderstand it. Is the pial surface same as gray matter? If not, how could I create a gray matter mask? Thanks,
Xiaomin
On Fri, Jan 15, 2016 at 9:31 AM -0800, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
I think you could easily hit all those voxels with a 1.5mm voxel size. Not sure what you are asking about in terms of gray matter.
On 01/15/2016 12:27 PM, Xiaomin Yue wrote:
The voxel size is 1.5mm. Some of voxels in the gray matter are not included in the mask as well. Why?
Xiaomin
On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That point is fairly close to the pial surface. What is your voxel size? It will include any voxel even if only a corner of it has some surface in it.
On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
here it is. thanks,
To: freesurfer@nmr.mgh.harvard.edu From: greve@nmr.mgh.harvard.edu Date: Fri, 15 Jan 2016 12:00:02 -0500 Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
it is hard to tell from that view. Can you click on a point that
appears
to be outside the brain so we can see what it looks like around that point in all three views?
On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
Hi All,
In fs5.3, I tried to generate a volume mask from the pial surface using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg $subjsess/bold/001/register.dof6.dat --template $subjsess/bold/001/template.nii --surf pial --o $subjsess/bold/001/lh.pialmask.vol.nii. The command run
successfully.
I doubled check the registration between the EPI and high resolution T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898. however, when I overlaid the mask on the T1.mgz, it is clear that some voxels outside brain are in the mask, and some voxels in the
gray
matter are not in the mask (see attached figure). Did I use the function incorrectly?
Thanks very much for your help.
Xiaomin
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 greve@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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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HelpLine at
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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 http://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
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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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The pial surface is the boundary between the gray matter and the tissue on the outside of the brain. It is not gray matter itself. If you want a mask of cortical gray matter, then use mri_label2vol --seg ribbon.mgz ..., then binarize the output of that to give you cortical GM.
On 01/15/2016 12:32 PM, Xiaomin Yue wrote:
Maybe, I misunderstand it. Is the pial surface same as gray matter? If not, how could I create a gray matter mask?
Thanks,
Xiaomin
On Fri, Jan 15, 2016 at 9:31 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think you could easily hit all those voxels with a 1.5mm voxel size. Not sure what you are asking about in terms of gray matter.
On 01/15/2016 12:27 PM, Xiaomin Yue wrote:
The voxel size is 1.5mm. Some of voxels in the gray matter are not included in the mask as well. Why?
Xiaomin
On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That point is fairly close to the pial surface. What is your voxel size? It will include any voxel even if only a corner of it has some surface in it.
On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
here it is. thanks,
To: freesurfer@nmr.mgh.harvard.edu From: greve@nmr.mgh.harvard.edu Date: Fri, 15 Jan 2016 12:00:02 -0500 Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
it is hard to tell from that view. Can you click on a point that
appears
to be outside the brain so we can see what it looks like around that point in all three views?
On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
Hi All,
In fs5.3, I tried to generate a volume mask from the pial surface using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg $subjsess/bold/001/register.dof6.dat --template $subjsess/bold/001/template.nii --surf pial --o $subjsess/bold/001/lh.pialmask.vol.nii. The command run
successfully.
I doubled check the registration between the EPI and high
resolution
T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898. however, when I overlaid the mask on the T1.mgz, it is clear that some voxels outside brain are in the mask, and some voxels in the
gray
matter are not in the mask (see attached figure). Did I use the function incorrectly?
Thanks very much for your help.
Xiaomin
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 greve@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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
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 greve@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 http://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or you can add --fillribbon to your surf2vol command (but the label2vol method is probably better)
On 01/15/2016 12:32 PM, Xiaomin Yue wrote:
Maybe, I misunderstand it. Is the pial surface same as gray matter? If not, how could I create a gray matter mask?
Thanks,
Xiaomin
On Fri, Jan 15, 2016 at 9:31 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think you could easily hit all those voxels with a 1.5mm voxel size. Not sure what you are asking about in terms of gray matter.
On 01/15/2016 12:27 PM, Xiaomin Yue wrote:
The voxel size is 1.5mm. Some of voxels in the gray matter are not included in the mask as well. Why?
Xiaomin
On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That point is fairly close to the pial surface. What is your voxel size? It will include any voxel even if only a corner of it has some surface in it.
On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
here it is. thanks,
To: freesurfer@nmr.mgh.harvard.edu From: greve@nmr.mgh.harvard.edu Date: Fri, 15 Jan 2016 12:00:02 -0500 Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
it is hard to tell from that view. Can you click on a point that
appears
to be outside the brain so we can see what it looks like around that point in all three views?
On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
Hi All,
In fs5.3, I tried to generate a volume mask from the pial surface using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg $subjsess/bold/001/register.dof6.dat --template $subjsess/bold/001/template.nii --surf pial --o $subjsess/bold/001/lh.pialmask.vol.nii. The command run
successfully.
I doubled check the registration between the EPI and high
resolution
T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898. however, when I overlaid the mask on the T1.mgz, it is clear that some voxels outside brain are in the mask, and some voxels in the
gray
matter are not in the mask (see attached figure). Did I use the function incorrectly?
Thanks very much for your help.
Xiaomin
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 greve@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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
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 greve@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 http://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks.
Xiaomin
On Fri, Jan 15, 2016 at 11:41 AM -0800, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
or you can add --fillribbon to your surf2vol command (but the label2vol method is probably better)
On 01/15/2016 12:32 PM, Xiaomin Yue wrote:
Maybe, I misunderstand it. Is the pial surface same as gray matter? If not, how could I create a gray matter mask?
Thanks,
Xiaomin
On Fri, Jan 15, 2016 at 9:31 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
I think you could easily hit all those voxels with a 1.5mm voxel size. Not sure what you are asking about in terms of gray matter.
On 01/15/2016 12:27 PM, Xiaomin Yue wrote:
The voxel size is 1.5mm. Some of voxels in the gray matter are not included in the mask as well. Why?
Xiaomin
On Fri, Jan 15, 2016 at 9:21 AM -0800, "Douglas N Greve" <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That point is fairly close to the pial surface. What is your voxel size? It will include any voxel even if only a corner of it has some surface in it.
On 01/15/2016 12:16 PM, Xiaomin Yue wrote:
here it is. thanks,
To: freesurfer@nmr.mgh.harvard.edu From: greve@nmr.mgh.harvard.edu Date: Fri, 15 Jan 2016 12:00:02 -0500 Subject: Re: [Freesurfer] mri_surf2vol {Disarmed}
it is hard to tell from that view. Can you click on a point that
appears
to be outside the brain so we can see what it looks like around that point in all three views?
On 01/15/2016 10:56 AM, Xiaomin Yue wrote:
Hi All,
In fs5.3, I tried to generate a volume mask from the pial surface using mri_surf2vol: mri_surf2vol --mkmask --hemi lh --reg $subjsess/bold/001/register.dof6.dat --template $subjsess/bold/001/template.nii --surf pial --o $subjsess/bold/001/lh.pialmask.vol.nii. The command run
successfully.
I doubled check the registration between the EPI and high
resolution
T1.mgz under the $SUBJECTS_DIR, which has the mincost at 0.3898. however, when I overlaid the mask on the T1.mgz, it is clear that some voxels outside brain are in the mask, and some voxels in the
gray
matter are not in the mask (see attached figure). Did I use the function incorrectly?
Thanks very much for your help.
Xiaomin
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 greve@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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://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
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 greve@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 http://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
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 greve@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
freesurfer@nmr.mgh.harvard.edu
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